# Siftome Ranked Dataset Export Active GEO index contains 47389 ranked datasets; organism mixed: Homo sapiens (35667), Mus musculus (11722); assay type mixed: microarray (24601), bulk RNA-seq (22787), other assay type (1). Rankings use the Tumor vs normal comparison with transparent suitability, metadata quality, and warning rules. Exploratory machine assessment; not a reviewed, frozen cohort or analysis approval. Study totals and cohort membership counts are not query-eligible sample counts. Unavailable eligibility evidence is unknown. Results are a starting point for review. Missing evidence leaves suitability unknown. ## Citation and Provenance - **Product:** Siftome - **Generated date:** 2026-10-28T14:19:35.875961307Z - **Citation text:** Generated with Siftome, a public omics dataset triage and metadata quality workflow tool. - **Original source citation reminder:** Cite original dataset sources when exported results are used in publications. - **Search criteria summary:** Patient tissue tumor-vs-normal; active defaults: none; user modifications: relaxed defaults: Human only; Bulk RNA-seq only; Tumor-normal only; Tissue or biopsy only; Hide biofluid/model systems; additional filters: Disease: Rheumatoid arthritis - **Structured search criteria:** searchIntent=patient-tissue-tumor-normal; recommendedOnly=false; excludeLowMetadataQuality=false; minimumSampleCount=none; processedDataAvailableOnly=false; hideCellLineDatasets=false; hideAmbiguousGroupings=false; matchedNormalOnly=false; geoOnly=false; recount3AvailableOnly=false; expressionAtlasAvailableOnly=false; trustedProcessedCountsAvailableOnly=false; tumorNormalOnly=false; tissueOrBiopsyOnly=false; hideBiofluidAndModelSystems=false; biofluidOnly=false; treatmentControlOnly=false; humanOnly=false; mouseOnly=false; bulkRnaSeqOnly=false; microarrayOnly=false; targetDiseaseContextOnly=false; includeBroaderGiAndMultiCancer=false; query=none; diseaseCondition=Rheumatoid arthritis; tissue=none; organism=none; assayType=none; modelType=none; anatomicalSource=none; specimenMaterial=none; cellPopulation=none - **Intent-specific ranking notice:** Recommendations are specific to the Patient tissue tumor-vs-normal intent and are not globally valid across all biological questions. - **Active organism expectation:** Homo sapiens - **Active assay expectation:** bulk RNA-seq - **Active default filters:** none - **User-modified filters:** relaxed defaults: Human only; Bulk RNA-seq only; Tumor-normal only; Tissue or biopsy only; Hide biofluid/model systems; additional filters: Disease: Rheumatoid arthritis - **Ranking batch:** 806958966744631c40063f0fc890965facdd40c0daba51edc35cd7d4956e097f - **Ranking batch ID:** d20028fc-f826-48f6-9cf2-e0eef07b824f - **Candidate generation version:** parent-series-search-candidates-v1 - **Candidate counts:** total=49115, parent=49115, secondary=0 - **Candidate set fingerprint:** d89295ea9fc12132672e2de3bcfe4afb86efc004cd3ab3c563538908e637a647 - **Search intent:** patient-tissue-tumor-normal - **Intent behavior version:** search-intent-behavior-v5 - **Scoring version:** intent-aware-scoring-v46 - **Normalization version:** sample-biological-dimensions-v26 - **Warning version:** intent-aware-warnings-v13 - **Ranking created at:** 2026-10-27T02:51:59.521293Z - **Source import or snapshot date:** Active GEO index snapshot for ranking batch 806958966744631c40063f0fc890965facdd40c0daba51edc35cd7d4956e097f - **Recommendation label definitions:** Recommended: strong first-pass triage candidate for the active criteria.; Useful with caution: potentially relevant but requires manual review of warnings and context.; Not suitable: not recommended for the active criteria without substantial manual justification.; Exploratory only: useful for discovery or review, not a direct recommendation. - **Recommendation-label meanings:** Recommended: strong first-pass triage candidate for the active criteria.; Useful with caution: potentially relevant but requires manual review of warnings and context.; Not suitable: not recommended for the active criteria without substantial manual justification.; Exploratory only: useful for discovery or review, not a direct recommendation. - **Known warning limitations:** Warnings are rule-based metadata signals, not a replacement for manual sample review before analysis. ## Search Criteria - **Search version:** tiered-discovery-search-v12 - **Scoring version:** intent-aware-scoring-v46 - **Intent behavior version:** search-intent-behavior-v5 - **Search intent:** Patient tissue tumor-vs-normal - **Intent-specific ranking notice:** Recommendations are specific to the Patient tissue tumor-vs-normal intent and are not globally valid across all biological questions. - **Intent wording:** Ranks human tissue tumor-vs-normal GEO datasets for suitability triage. - **Active organism expectation:** Homo sapiens - **Active assay expectation:** bulk RNA-seq - **Active default filters:** none - **User-modified filters:** relaxed defaults: Human only; Bulk RNA-seq only; Tumor-normal only; Tissue or biopsy only; Hide biofluid/model systems; additional filters: Disease: Rheumatoid arthritis - **Active assay mix:** bulk RNA-seq - **Active default filter state:** {"labels": ["Human only", "Bulk RNA-seq only", "Tumor-normal only", "Tissue or biopsy only", "Hide biofluid/model systems"], "summary": "Human only; Bulk RNA-seq only; Tumor-normal only; Tissue or biopsy only; Hide biofluid/model systems", "humanOnly": true, "mouseOnly": false, "biofluidOnly": false, "bulkRnaSeqOnly": true, "microarrayOnly": false, "recommendedOnly": false, "tumorNormalOnly": true, "matchedNormalOnly": false, "tissueOrBiopsyOnly": true, "treatmentControlOnly": false, "targetDiseaseContextOnly": false, "hideBiofluidAndModelSystems": true} - **Allowed study designs:** tumor vs matched normal or tumor vs unmatched normal - **Recommendation meaning:** Recommended means a human bulk RNA-seq tissue or biopsy cohort with clear tumor-normal grouping and sufficient metadata for first-pass triage. - **Recommendation-label meanings:** Recommended: strong first-pass triage candidate for the active criteria.; Useful with caution: potentially relevant but requires manual review of warnings and context.; Not suitable: not recommended for the active criteria without substantial manual justification.; Exploratory only: useful for discovery or review, not a direct recommendation. - **Known warning limitations:** Warnings are rule-based metadata signals, not a replacement for manual sample review before analysis. - **Source:** GEO - **Active index organism:** mixed: Homo sapiens (35667), Mus musculus (11722) - **Active index assay type:** mixed: microarray (24601), bulk RNA-seq (22787), other assay type (1) - **Search use case:** Ranks human tissue tumor-vs-normal GEO datasets for suitability triage. - **Minimum sample count:** none - **Processed data available only:** false - **Required metadata:** usable sample-level metadata - **Disallowed contexts:** microarray unless explicitly enabled, biofluid-only datasets, cell-line datasets, organoid datasets, xenograft or PDX datasets, or treatment-only experiments ## Ranked Datasets | Rank | Dataset | Title | Unmet criteria | Design | Specimen | Scores | Warnings | Source | Recommendation | | ---: | --- | --- | --- | --- | --- | --- | --- | --- | --- | | 1 | [GSE101193](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE101193) | Identify the expression of lncRNAs in peripheral blood mononuclear cells from rheumatoid arthritis | none | Patient biofluid vs healthy control | Biofluid | suitability 20; metadata 100; overall 45 | SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE101193) | Exploratory only | | 2 | [GSE169082](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE169082) | Transcriptome Analysis of PBMCs in peripheral blood of patients with RA | none | Patient biofluid vs healthy control | Biofluid | suitability 20; metadata 100; overall 45 | SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE169082) | Exploratory only | | 3 | [GSE294225](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294225) | Transcriptional profiles are dramatically altered in circulating CD14+ monocytes in Rheumatoid Arthritis [RNA-seq] | none | Patient biofluid vs healthy control | Biofluid | suitability 20; metadata 100; overall 45 | none | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE294225) | Exploratory only | | 4 | [GSE93272](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93272) | Whole blood gene expression of rheumatoid arthritis | none | Patient biofluid vs healthy control | Biofluid | suitability 20; metadata 100; overall 45 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93272) | Exploratory only | | 5 | [GSE110169](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110169) | BMS_TRD_SLE_RA_WB_study | none | Patient biofluid vs healthy control | Biofluid | suitability 10; metadata 100; overall 45 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110169) | Exploratory only | | 6 | [GSE17755](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17755) | Human peripheral blood cells: autoimmune diseases vs. healthy individuals | none | Patient biofluid vs healthy control | Biofluid | suitability 10; metadata 100; overall 45 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17755) | Exploratory only | | 7 | [GSE10500](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10500) | Gene expression in rheumatoid arthritis synovial macrophages | none | Disease/model vs control | Biofluid | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10500) | Not suitable | | 8 | [GSE111946](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111946) | microRNA-218 modulates gene expression in fibroblast-like synovial cells in rheumatoid arthritis | none | Disease/model vs control | Tissue | suitability 0; metadata 100; overall 34 | SMALL_COHORT_NEEDS_REVIEW [warning]: Dataset has fewer than six samples and should not be treated as a high-confidence cohort without manual review.; SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111946) | Not suitable | | 9 | [GSE12021](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12021) | Identification of inter-individual and gene-specific variances in mRNA expression profiles in the RA SM | none | Disease/model vs control | Tissue | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12021) | Not suitable | | 10 | [GSE121894](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE121894) | Gene expression profile of endothelial cells derived from circulating progenitors issued from patients with rheumatoid arthritis | none | Disease/model vs control | Biofluid | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE121894) | Not suitable | | 11 | [GSE128813](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE128813) | The transcriptome analysis of regulatory networks in RA-FLSs | none | Disease/model vs control | Cell line | suitability 0; metadata 100; overall 34 | MIXED_SAMPLE_TYPES [warning]: Multiple sample type labels or exclusion flags were detected.; CELL_LINES_INCLUDED [warning]: Cell line samples appear to be included.; SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE128813) | Not suitable | | 12 | [GSE13026](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13026) | Early and long-standing rheumatoid arthritis: molecular signatures identified by gene expression profiling in synovium | none | Disease/model vs control | Unclear specimen/source | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13026) | Not suitable | | 13 | [GSE133426](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE133426) | Human memory Th17 cell populations change into anti-inflammatory cells with regulatory capacity upon exposure to active Vitamin D | none | Treatment vs control | Unclear specimen/source | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE133426) | Not suitable | | 14 | [GSE134087](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134087) | Analysis of differential expression profiles of Long noncoding RNA in peripheral blood of patients with active rheumatoid arthritis | none | Patient biofluid vs healthy control | Biofluid | suitability 0; metadata 100; overall 34 | SMALL_COHORT_NEEDS_REVIEW [warning]: Dataset has fewer than six samples and should not be treated as a high-confidence cohort without manual review.; SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134087) | Not suitable | | 15 | [GSE1402](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1402) | Juvenile Rheumatoid Arthritis Profiles In PBMC and SFMC | none | Disease/model vs control | Biofluid | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1402) | Not suitable | | 16 | [GSE141934](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE141934) | Transcriptional data of inflamatory arthritis T cells. | none | Disease/model vs control | Biofluid | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; THIRD_PARTY_REANALYSIS [warning]: This record is a third-party integration or reanalysis of public datasets. The GEO sample count may describe deposited atlas records rather than one independent clinical cohort; verify source-study provenance before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE141934) | Not suitable | | 17 | [GSE142049](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE142049) | Transcriptional data of inflamatory arthritis B cells | none | Disease/model vs control | Biofluid | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; THIRD_PARTY_REANALYSIS [warning]: This record is a third-party integration or reanalysis of public datasets. The GEO sample count may describe deposited atlas records rather than one independent clinical cohort; verify source-study provenance before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE142049) | Not suitable | | 18 | [GSE142607](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE142607) | Metabolism in synovial macrophages are reprogrammed by synovial fibroblasts under inflammatory condition | none | Disease/model vs control | Tissue | suitability 0; metadata 100; overall 34 | INTENT_ASSAY_MISMATCH [critical]: Dataset organism does not match the human patient-tissue tumor-normal intent. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE142607) | Not suitable | | 19 | [GSE148395](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE148395) | Effect of BET Inhibitors on Rheumatoid Synovial Fibroblast Cells [RNA-seq] | none | Treatment vs control | Unclear specimen/source | suitability 0; metadata 100; overall 34 | INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE148395) | Not suitable | | 20 | [GSE153378](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE153378) | Expression data (U133 Plus 2.0) from fibroblast like synoviocytes from patients with rheumatoid arthritis (RA-FLS) stimulated by FasL | none | Treatment vs control | Tissue | suitability 0; metadata 100; overall 34 | TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE153378) | Not suitable | | 21 | [GSE15573](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15573) | Immunity and Defense Genes in Peripheral Blood Mononuclear Cells of Rheumatoid Arthritis patients | none | Disease/model vs control | Biofluid | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15573) | Not suitable | | 22 | [GSE157047](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE157047) | Interplay of NLRC4/NLRP3 inflammasomes and Fc-ˠ-Receptors on CD1c+ DC Associates with Pathogenic IFNˠ+IL17+ T cells and RA Severity | none | Disease/model vs control | Mixed specimen/source | suitability 0; metadata 100; overall 34 | MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE157047) | Not suitable | | 23 | [GSE181614](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE181614) | RNA Sequencing facilitates quantitative analysis of lncRNA and mRNA expression in fibroblast-like synoviocytes from rheumatoid arthritis patients and trauma patients [microarray] | none | Disease/model vs control | Tissue | suitability 0; metadata 100; overall 34 | SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE181614) | Not suitable | | 24 | [GSE189136](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE189136) | Targeting MyD88 Downregulates Inflammatory Mediators and Pathogenic Processes in PBMC From DMARDs-Naïve Rheumatoid Arthritis Patients | none | Treatment vs control | Biofluid | suitability 0; metadata 100; overall 34 | none | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE189136) | Not suitable | | 25 | [GSE189338](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE189338) | Expression profile of circRNA in peripheral blood mononuclear cells of patients with rheumatoid arthritis | none | Patient biofluid vs healthy control | Biofluid | suitability 0; metadata 100; overall 34 | SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE189338) | Not suitable | | 26 | [GSE1919](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1919) | Rheumatoid arthritis | none | Disease/model vs control | Unclear specimen/source | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1919) | Not suitable | | 27 | [GSE195557](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE195557) | TNFR2 is critical for TNF-induced rheumatoid arthritis fibroblast-like synoviocyte inflammation | none | Treatment vs control | Tissue | suitability 0; metadata 100; overall 34 | none | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE195557) | Not suitable | | 28 | [GSE197057](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE197057) | Expression data (U133 Plus 2.0) from fibroblast like synoviocytes from patients with rheumatoid arthritis (RA-FLS) stimulated by LIGHT. | none | Treatment vs control | Unclear specimen/source | suitability 0; metadata 100; overall 34 | TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE197057) | Not suitable | | 29 | [GSE200291](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE200291) | Effect of anti-TNF/IL-6 NANOBODY® VHH, Humira, Sylvant, TNF, IL6 and TNF+IL6 in RA-FLS/T cell cocultures | none | Treatment vs control | Biofluid | suitability 0; metadata 100; overall 34 | TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison.; TREATED_AND_UNTREATED_SAMPLES_MIXED [info]: Treated and untreated samples are both present. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE200291) | Not suitable | | 30 | [GSE2053](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2053) | RAvs.ND | none | Disease/model vs control | Unclear specimen/source | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2053) | Not suitable | | 31 | [GSE205795](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE205795) | Effect of Schisandrin on Rheumatoid Synovial Fibroblast-like Synoviocytes | none | Treatment vs control | Tissue | suitability 0; metadata 100; overall 34 | none | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE205795) | Not suitable | | 32 | [GSE205962](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE205962) | Expression data from whole blood sample of eight kinds of TCM syndromes of rheumatoid arthritis patients. | none | Patient biofluid vs healthy control | Biofluid | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE205962) | Not suitable | | 33 | [GSE206848](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE206848) | Dysregulated gene expression in human osteoarthritic (OA) and rheumatoid arthritis (RA) synovium | none | Disease/model vs control | Tissue | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE206848) | Not suitable | | 34 | [GSE213842](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE213842) | Comprehensive analysis and functional characteristics of differential expression of N6-methyladenosine methylation modification in the whole transcriptome of rheumatoid arthritis | none | Disease/model vs control | Tissue | suitability 0; metadata 100; overall 34 | none | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE213842) | Not suitable | | 35 | [GSE217012](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE217012) | MYD88 dimerization controls the proliferative, invasive, and pro-inflammatory responses of synovial fibroblasts from rheumatoid arthritis patients | none | Treatment vs control | Tissue | suitability 0; metadata 100; overall 34 | MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE217012) | Not suitable | | 36 | [GSE21959](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21959) | Transcriptional response to hypoxia of normal and rheumatoid arthritis synovial fibroblasts | none | Disease/model vs control | Unclear specimen/source | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21959) | Not suitable | | 37 | [GSE23561](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23561) | Peripheral blood gene expression profiles in metabolic syndrome, coronary artery disease and type 2 diabetes | none | Disease/model vs control | Biofluid | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23561) | Not suitable | | 38 | [GSE236924](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE236924) | SIRPa agonist antibody treatment ameliorates experimental arthritis and colitis [array] | none | Disease/model vs control | Tissue | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE236924) | Not suitable | | 39 | [GSE24742](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24742) | Effects of Rituximab on global gene expression profiles in the RA synovium | none | Treatment vs control | Biopsy | suitability 0; metadata 100; overall 34 | TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison.; TREATED_AND_UNTREATED_SAMPLES_MIXED [info]: Treated and untreated samples are both present.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24742) | Not suitable | | 40 | [GSE290552](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE290552) | Mapping the Molecular Signature of Progressive Multiple Sclerosis [197191] | none | Treatment vs control | Cell line | suitability 0; metadata 100; overall 34 | MIXED_SAMPLE_TYPES [warning]: Multiple sample type labels or exclusion flags were detected.; CELL_LINES_INCLUDED [warning]: Cell line samples appear to be included.; TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE290552) | Not suitable | | 41 | [GSE29746](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29746) | Transcriptional analysis of normal and pathological synovial fibroblasts | none | Disease/model vs control | Unclear specimen/source | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29746) | Not suitable | | 42 | [GSE301891](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE301891) | RNA-Seq Analysis of Fibroblast-Like Synoviocytes Treated With Lutein in a Rheumatoid Arthritis Context | none | Treatment vs control | Cell line | suitability 0; metadata 100; overall 34 | MIXED_SAMPLE_TYPES [warning]: Multiple sample type labels or exclusion flags were detected.; CELL_LINES_INCLUDED [warning]: Cell line samples appear to be included. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE301891) | Not suitable | | 43 | [GSE34391](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34391) | A pilot study of circulating miRNAs as potiential biomarkers in patients with system lupus erythematosus | none | Treatment vs control | Biofluid | suitability 0; metadata 100; overall 34 | TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison.; SAMPLE_COUNT_BELOW_THRESHOLD [warning]: Total sample count is below the minimum needed for two comparison groups.; SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34391) | Not suitable | | 44 | [GSE4255](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4255) | Pooled B-Cell C441MC-C442MC | none | Disease/model vs control | Tissue | suitability 0; metadata 100; overall 34 | SAMPLE_COUNT_BELOW_THRESHOLD [warning]: Total sample count is below the minimum needed for two comparison groups.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4255) | Not suitable | | 45 | [GSE45867](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45867) | Effects of tocilizumab versus methotrexate therapy on gene expression profiles in the early rheumatoid arthrtis synovium | none | Treatment vs control | Tissue | suitability 0; metadata 100; overall 34 | TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison.; TREATED_AND_UNTREATED_SAMPLES_MIXED [info]: Treated and untreated samples are both present.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45867) | Not suitable | | 46 | [GSE55235](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE55235) | Identification of rheumatoid arthritis and osteoarthritis patients by transcriptome-based rule set generation | none | Disease/model vs control | Tissue | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE55235) | Not suitable | | 47 | [GSE55457](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE55457) | Identification of rheumatoid arthritis and osteoarthritis patients by transcriptome-based rule set generation [Jena] | none | Disease/model vs control | Tissue | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE55457) | Not suitable | | 48 | [GSE56649](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE56649) | Expression data from active rheumatoid arthritis patients and healthy control. | none | Patient biofluid vs healthy control | Biofluid | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE56649) | Not suitable | | 49 | [GSE57376](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57376) | Synovial biopsies from RA and PsA patients and skin biopsies from Psoriasis patients under Infliximab treatment | none | Disease/model vs control | Biopsy | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57376) | Not suitable | | 50 | [GSE57383](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57383) | Gene expression of CD14+ cells from RA, PsA and PsO patients with Infliximab treatment | none | Disease/model vs control | Unclear specimen/source | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57383) | Not suitable | | 51 | [GSE57405](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57405) | Gene expression of CD14- cells from RA, PsA and PsO patients with Infliximab treatment | none | Disease/model vs control | Unclear specimen/source | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57405) | Not suitable | | 52 | [GSE63995](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63995) | Expression data (U133 Plus 2.0) from fibroblast like synoviocytes from patients with rheumatoid arthritis (RA-FLS) stimulated by TL1A | none | Treatment vs control | Unclear specimen/source | suitability 0; metadata 100; overall 34 | TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison.; TREATED_AND_UNTREATED_SAMPLES_MIXED [info]: Treated and untreated samples are both present.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63995) | Not suitable | | 53 | [GSE65010](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65010) | Gene expression profiling of effector and regulatory T-cells from peripheral blood of rheumatoid arthritis (RA) patients and healthy volunteers. | none | Disease/model vs control | Unclear specimen/source | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65010) | Not suitable | | 54 | [GSE71370](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71370) | Profiling of CD14+ monocytes from paired rheumatoid arthritis (RA)-patient peripheral blood and synovial fluid samples | none | Patient biofluid vs healthy control | Biofluid | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71370) | Not suitable | | 55 | [GSE77298](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE77298) | Synovial biopsies of rheumatoid arthritis and healthy controls | none | Disease/model vs control | Tissue | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE77298) | Not suitable | | 56 | [GSE83147](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE83147) | RNA expression profiles in fibroblast-like synoviocytes from rheumatoid arthritis patients and trauma patients | none | Disease/model vs control | Unclear specimen/source | suitability 0; metadata 100; overall 34 | SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE83147) | Not suitable | | 57 | [GSE84074](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84074) | Rheumatoid arthritis and response to LLDT-8: Fibroblast-like Synoviocytes | none | Treatment vs control | Biopsy | suitability 0; metadata 100; overall 34 | TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison.; SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84074) | Not suitable | | 58 | [GSE93720](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93720) | Transcriptional response of human synovial fibroblasts to TNF and IL-17A (Microarray Data 2) | none | Disease/model vs control | Tissue | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93720) | Not suitable | | 59 | [GSE93776](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93776) | Immune cells gene expression from rheumatoid arthritis and healthy donors | none | Disease/model vs control | Unclear specimen/source | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93776) | Not suitable | | 60 | [GSE97779](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97779) | Expression data from rheumatoid arthritis synovial macrophages | none | Disease/model vs control | Mixed specimen/source | suitability 0; metadata 100; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE97779) | Not suitable | | 61 | [GSE100648](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100648) | Early arthritis B cell gene expression profiling | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100648) | Not suitable | | 62 | [GSE100786](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100786) | Expression data of bone marrow and blood monocytes from patients with rheumatoid arthritis (RA) and osteoarthritis (OA) | none | Unclear study design | Mixed specimen/source | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100786) | Not suitable | | 63 | [GSE103578](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE103578) | lncRNA and mRNA expression profiles in fibroblast-like synoviocytes from rheumatoid arthritis patients and trauma patients | none | Unclear study design | Tissue | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE103578) | Not suitable | | 64 | [GSE107105](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE107105) | Microarray analysis of freshly isolated synovial fibroblast subsets in patients with rheumatoid arthritis or osteoarthritis | none | Unclear study design | Unclear specimen/source | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE107105) | Not suitable | | 65 | [GSE109448](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE109448) | RNA-seq analysis of freshly isolated synovial fibroblast subsets from patients with rheumatoid arthritis | none | Unclear study design | Unclear specimen/source | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE109448) | Not suitable | | 66 | [GSE112809](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE112809) | Treatment of rheumatoid arthritis patients with chaperonin 10 | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE112809) | Not suitable | | 67 | [GSE12051](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12051) | Microarray predictor of response to infliximab in rheumatoid arthritis (RA) patients | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12051) | Not suitable | | 68 | [GSE122624](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE122624) | RORγt inhibition selectively targets IL-17 producing human iNKT and γδ-T cells enriched in Spondyloarthritis while preserving IL-22 responses | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE122624) | Not suitable | | 69 | [GSE12653](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12653) | Gene Expression Analysis in Peripheral Blood of Patients with Rheumatoid Arthritis | none | Unclear study design | Unclear specimen/source | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12653) | Not suitable | | 70 | [GSE129486](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE129486) | Transcriptional responses of human synovial fibroblasts to TNF and IL-17A over time (RNA-seq Data 1) | none | Unclear study design | Tissue | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE129486) | Not suitable | | 71 | [GSE129705](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE129705) | RNA-sequencing of whole blood samples from biologic naïve rheumatoid arthritis patients initiating anti-TNF treatment | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE129705) | Not suitable | | 72 | [GSE132832](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132832) | Impaired ATM Activation in B Cells Promotes Osteoclastogenic Cytokine Production and Bone Erosion in Patients with Rheumatoid Arthritis | none | Unclear study design | Unclear specimen/source | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132832) | Not suitable | | 73 | [GSE13917](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13917) | Complement receptor 2/CD21– human naive B cells contain mostly autoreactive unresponsive clones | none | Unclear study design | Unclear specimen/source | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13917) | Not suitable | | 74 | [GSE140036](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE140036) | Microarray analysis of the synovial membrane of rheumatoid arthritis patients undergoing anti-TNF therapy | none | Unclear study design | Unclear specimen/source | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE140036) | Not suitable | | 75 | [GSE146393](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146393) | MicroRNA microarray of CD8+ T cells | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146393) | Not suitable | | 76 | [GSE15258](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15258) | Whole blood transcript profiling of rheumatoid arthritis patients | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15258) | Not suitable | | 77 | [GSE153015](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE153015) | Comparison of gene expression profiles in paired synovial biopsies from rheumatoid arthritis (RA) patients | none | Unclear study design | Tissue | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE153015) | Not suitable | | 78 | [GSE15316](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15316) | Differential expression of rituximab responders vs. non responders on 3 different blood cell types | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15316) | Not suitable | | 79 | [GSE15602](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15602) | Differential gene expression in RA synovial biopsies from responders versus non-responders to adalimumab therapy | none | Unclear study design | Biopsy | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15602) | Not suitable | | 80 | [GSE15615](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15615) | Differential effects of TNFalpha and IL1beta on FLS global gene expression profile | none | Unclear study design | Cultured cells | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; CULTURED_CELL_MODEL_NEEDS_REVIEW [warning]: Cultured primary, endothelial, macrophage, or stem-cell samples were detected; interpret these as an experimental model rather than a patient biofluid or tissue cohort.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15615) | Not suitable | | 81 | [GSE172188](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE172188) | Rheumatoid arthritis synovium response to abatacept | none | Unclear study design | Tissue | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE172188) | Not suitable | | 82 | [GSE176440](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE176440) | Gene expression profiles of CD4+ T cells before and after methotrexate treatment in rheumatoid arthritis patients [Microarray] | none | Unclear study design | Unclear specimen/source | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE176440) | Not suitable | | 83 | [GSE18097](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18097) | Comparison of miRNA from healthy donors versus Rheumatoid arthritis patients | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | SAMPLE_COUNT_BELOW_THRESHOLD [warning]: Total sample count is below the minimum needed for two comparison groups.; SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE18097) | Not suitable | | 84 | [GSE199152](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE199152) | Next Generation Sequencing Quantitative Analysis of RA-UIP, IPF-UIP, and Non-UIP Patient Lung Biopsy Transcriptomes | none | Unclear study design | Biopsy | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE199152) | Not suitable | | 85 | [GSE21385](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21385) | Culture effects on rheumatoid arthrits synovial fibroblasts | none | Unclear study design | Tissue | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; PROCESSED_COUNTS_NOT_FOUND [warning]: Processed count data was not found in the dataset index.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21385) | Not suitable | | 86 | [GSE21537](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21537) | The relationship between the gene expression profile in the synovium of RA patients at baseline and the clinical response to infliximab treatment | none | Unclear study design | Biopsy | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21537) | Not suitable | | 87 | [GSE224842](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE224842) | Gene expression profiles of peripheral blood mononuclear cells before abatacept treatment in rheumatoid arthritis patients. | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE224842) | Not suitable | | 88 | [GSE225731](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE225731) | Disease activity drives transcriptomic heterogeneity in early untreated rheumatoid synovitis | none | Unclear study design | Tissue | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE225731) | Not suitable | | 89 | [GSE261149](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE261149) | Ginsenoside compound K plays an anti-inflammatory effect without inducing glucose metabolism disorder in adjuvant-induced arthritis rats [human] | none | Unclear study design | Tissue | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE261149) | Not suitable | | 90 | [GSE263015](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE263015) | MicroRNA expression profiling of synovial fluid in early and late Osteoarthritis and comparison with Rheumatoid Arthritis | none | Unclear study design | Unclear specimen/source | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE263015) | Not suitable | | 91 | [GSE27390](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27390) | Human bone marrow-derived mononuclear cells (BMMC): rheumatoid arthritis vs. osteoarthritis | none | Unclear study design | Tissue | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27390) | Not suitable | | 92 | [GSE279719](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE279719) | Human CD14+ monocytes from early inflammatory arthritis patients before and after a 5day-and 30day-period of methotrexate treatment | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE279719) | Not suitable | | 93 | [GSE30023](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30023) | A comparative gene expression profiling of spondyloarthropathy and rheumatoid arthritis using oligonucleotide based microarrays | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30023) | Not suitable | | 94 | [GSE311923](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE311923) | Role of m⁶A-Modified GAS6 in Rheumatoid Arthritis: Insights from Multi-Omics Analysis | none | Unclear study design | Tissue | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE311923) | Not suitable | | 95 | [GSE31685](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31685) | The influence of resveratrol on rheumatoid fibroblast-like synoviocytes based on a gene chip transcription analysis | none | Unclear study design | Cultured cells | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; CULTURED_CELL_MODEL_NEEDS_REVIEW [warning]: Cultured primary, endothelial, macrophage, or stem-cell samples were detected; interpret these as an experimental model rather than a patient biofluid or tissue cohort.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31685) | Not suitable | | 96 | [GSE35455](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE35455) | Human peripheral blood cells (PB): Effect of Tocilizumab/MRA compared to methotrexate(MTX) treatments on rheumatoid arthritis(RA) patients. | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE35455) | Not suitable | | 97 | [GSE36700](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36700) | Gene expression profiles in synovial biopsies from patients with arthritis | none | Unclear study design | Tissue | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36700) | Not suitable | | 98 | [GSE36757](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36757) | Human Rheumatoid Arthritis Synovial Fibroblasts: Control vs. Tenascin-C Stimulated | none | Unclear study design | Tissue | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison.; SAMPLE_COUNT_BELOW_THRESHOLD [warning]: Total sample count is below the minimum needed for two comparison groups.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36757) | Not suitable | | 99 | [GSE37107](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37107) | Genome-wide transcription analysis of whole blood prior to rituximab treatment in relation to clinical response | none | Treatment vs control | Biofluid | suitability 0; metadata 93; overall 34 | TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison.; TREATED_AND_UNTREATED_SAMPLES_MIXED [info]: Treated and untreated samples are both present.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37107) | Not suitable | | 100 | [GSE38064](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38064) | Expression data of subtypes of inflamed synovia from patients with rheumatoid arthritis | none | Unclear study design | Tissue | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38064) | Not suitable | | 101 | [GSE39340](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39340) | Indentification of special gene expressions in synovial tissues of rheumatoid arthritis | none | Unclear study design | Tissue | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39340) | Not suitable | | 102 | [GSE42296](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42296) | Distinct, non-overlapping gene panels of peripheral blood gene expression predict response to infliximab therapy in rheumatoid arthritis and Crohn's disease | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42296) | Not suitable | | 103 | [GSE42842](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42842) | The predictive biomarkers of TNFα-blocking agent responsiveness are specific for adalimumab and etanercept | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42842) | Not suitable | | 104 | [GSE4588](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4588) | Identification of genes specifically over-expressed in lupus CD4 T and B cells | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4588) | Not suitable | | 105 | [GSE47726](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47726) | Genome-wide transcriptional analysis of synovial tissue gene expression associated with the response to anti-TNF therapy in Rheumatoid Arthritis | none | Unclear study design | Unclear specimen/source | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47726) | Not suitable | | 106 | [GSE48780](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE48780) | Expression data from Rheumatoid Arthritis synovial tissue samples | none | Unclear study design | Mixed specimen/source | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE48780) | Not suitable | | 107 | [GSE55584](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE55584) | Identification of rheumatoid arthritis and osteoarthritis patients by transcriptome-based rule set generation [Leipzig] | none | Unclear study design | Tissue | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE55584) | Not suitable | | 108 | [GSE56409](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE56409) | Stromal transcriptional profiles reveal hierarchies of anatomical site, serum response and disease and identify disease specific pathways | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE56409) | Not suitable | | 109 | [GSE59526](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59526) | Affymetrix Chip data of the transcriptome of human clinical study for acupuncture mechanisms on rheumatoid arthritis | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59526) | Not suitable | | 110 | [GSE60649](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60649) | Myeloid malignancies with chromosome 5q deletions acquire a dependency on an intrachromosomal NF-κB gene network | none | Unclear study design | Tissue | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60649) | Not suitable | | 111 | [GSE66084](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE66084) | Characteristic expression of MSX1, MSX2, TBX2, and ENTPD1 in dental pulp cells | none | Unclear study design | Tissue | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE66084) | Not suitable | | 112 | [GSE72258](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72258) | Microarray data for Rheumatoid arthritis synovial fibroblast (RASF) after C5orf30 and HDAC1 knockdown | none | Unclear study design | Tissue | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72258) | Not suitable | | 113 | [GSE73764](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73764) | Transcriptomic effects of TNFa in primary fibroblast-like synovial cell cultures | none | Unclear study design | Tissue | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison.; SMALL_COHORT_NEEDS_REVIEW [warning]: Dataset has fewer than six samples and should not be treated as a high-confidence cohort without manual review.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73764) | Not suitable | | 114 | [GSE74143](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE74143) | Whole blood gene expression from subjects with moderate to severe rheumatoid arthritis | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE74143) | Not suitable | | 115 | [GSE7524](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7524) | Expression profiling in RA disease pre and post anti-TNF treatment | none | Unclear study design | Unclear specimen/source | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7524) | Not suitable | | 116 | [GSE78068](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE78068) | Identification of baseline gene expression signatures predicting therapeutic responses to three biologic agents in rheumatoid arthritis: a retrospective observational study | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE78068) | Not suitable | | 117 | [GSE80785](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE80785) | Gene expressions of CD4+ T cells from patients with rheumatoid arthritis in each developmental stages | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE80785) | Not suitable | | 118 | [GSE91026](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE91026) | Global miRNA expression profiles of fibroblast-like synoviocytes in patients with rheumatoid arthritis and osteoarthritis | none | Unclear study design | Unclear specimen/source | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison.; SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE91026) | Not suitable | | 119 | [GSE9329](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9329) | Expression data of synovial cells isolated from patients with rheumatoid arthritis | none | Unclear study design | Tissue | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; SAMPLE_COUNT_BELOW_THRESHOLD [warning]: Total sample count is below the minimum needed for two comparison groups.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9329) | Not suitable | | 120 | [GSE93698](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93698) | Gene expression profiles in systemic sclerosis tenosynovial biopsies | none | Unclear study design | Biopsy | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE93698) | Not suitable | | 121 | [GSE94897](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE94897) | B cells expressing the IgA receptor FcRL4 participate in the autoimmune response in patients with rheumatoid arthritis | none | Unclear study design | Biofluid | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE94897) | Not suitable | | 122 | [GSE38351](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38351) | The multifaceted balance of TNF-a and type I / II interferon responses in SLE and RA: how monocytes manage the impact of cytokines | none | Treatment vs control | Biofluid | suitability 0; metadata 90; overall 34 | TECHNICAL_REPLICATES_DETECTED [warning]: Technical replicate samples were detected.; TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38351) | Not suitable | | 123 | [GSE118958](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE118958) | Expression data (U133 Plus 2.0) from fibroblast like synoviocytes from patients with rheumatoid arthritis (RA-FLS) stimulated by TL1A | none | Treatment vs control | Unclear specimen/source | suitability 0; metadata 85; overall 34 | TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; TISSUE_TYPE_MISSING [warning]: Tissue or cell type could not be normalized.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE118958) | Not suitable | | 124 | [GSE145204](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE145204) | Transcriptional responses to TNF following HFl treatment of primary rheumatoid arthritis fibroblast like synoviocytes (RA-FLS) | none | Treatment vs control | Unclear specimen/source | suitability 0; metadata 85; overall 34 | TISSUE_TYPE_MISSING [warning]: Tissue or cell type could not be normalized.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE145204) | Not suitable | | 125 | [GSE200030](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE200030) | Regulation of type I interferon signature by VGLL3 in the fibroblast-like synoviocytes of rheumatoid arthritis patients via targeting the Hippo pathway | none | Disease/model vs control | Unclear specimen/source | suitability 0; metadata 85; overall 34 | SAMPLE_COUNT_BELOW_THRESHOLD [warning]: Total sample count is below the minimum needed for two comparison groups.; TISSUE_TYPE_MISSING [warning]: Tissue or cell type could not be normalized.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE200030) | Not suitable | | 126 | [GSE22956](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22956) | NFAT5 is a critical regulator of rheumatoid inflammation | none | Disease/model vs control | Unclear specimen/source | suitability 0; metadata 85; overall 34 | MIXED_SAMPLE_TYPES [warning]: Multiple sample type labels or exclusion flags were detected.; CELL_LINES_INCLUDED [warning]: Cell line samples appear to be included.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; TISSUE_TYPE_MISSING [warning]: Tissue or cell type could not be normalized.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22956) | Not suitable | | 127 | [GSE266310](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE266310) | Effects of methotrexate and tofacitinib on gene expression of activated rheumatoid arthritis fibroblast-like synoviocytes | none | Treatment vs control | Unclear specimen/source | suitability 0; metadata 85; overall 34 | TISSUE_TYPE_MISSING [warning]: Tissue or cell type could not be normalized.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE266310) | Not suitable | | 128 | [GSE2779](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2779) | Gene expression profile of normal v early MDS v non-MDS anemia bone marrow CD34 cells | none | Disease/model vs control | Unclear specimen/source | suitability 0; metadata 85; overall 34 | MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; TISSUE_TYPE_MISSING [warning]: Tissue or cell type could not be normalized.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2779) | Not suitable | | 129 | [GSE300831](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE300831) | RNA-seq of Immortalized RAFLS treated with TNFα for 24h and DMSO or celastrol derivatives for 4h in human | none | Treatment vs control | Cell line | suitability 0; metadata 85; overall 34 | MIXED_SAMPLE_TYPES [warning]: Multiple sample type labels or exclusion flags were detected.; CELL_LINES_INCLUDED [warning]: Cell line samples appear to be included. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE300831) | Not suitable | | 130 | [GSE45665](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45665) | Expression data (U133 Plus 2.0) from fibroblast like synoviocytes from patients with rheumatoid arthritis (RA-FLS) stimulated by DcR3 | none | Treatment vs control | Tissue | suitability 0; metadata 85; overall 34 | TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45665) | Not suitable | | 131 | [GSE94519](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE94519) | Long noncoding RNAs expression profile in patients with rheumatoid arthritis | none | Patient biofluid vs healthy control | Biofluid | suitability 0; metadata 85; overall 34 | SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE94519) | Not suitable | | 132 | [GSE243821](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE243821) | LncRNA of human Fibroblast-like synoviocytes of rheumatoid arthritis and osteoarthritis | none | Unclear study design | Unclear specimen/source | suitability 0; metadata 78; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; TISSUE_TYPE_MISSING [warning]: Tissue or cell type could not be normalized.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE243821) | Not suitable | | 133 | [GSE267979](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE267979) | Temporal artery biopsy of Giant cell arteritis | none | Unclear study design | Biopsy | suitability 0; metadata 78; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE267979) | Not suitable | | 134 | [GSE33377](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE33377) | Expression profiling of rheumatoid arthritis patients treated with anti-TNF | none | Unclear study design | Unclear specimen/source | suitability 0; metadata 78; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; TISSUE_TYPE_MISSING [warning]: Tissue or cell type could not be normalized.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE33377) | Not suitable | | 135 | [GSE37427](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37427) | Expression data from fibroblast-like synoviocytes (FLS) transfected with mimic-miR-23b or mimic-NC | none | Unclear study design | Unclear specimen/source | suitability 0; metadata 78; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; SAMPLE_COUNT_BELOW_THRESHOLD [warning]: Total sample count is below the minimum needed for two comparison groups.; SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; TISSUE_TYPE_MISSING [warning]: Tissue or cell type could not be normalized.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37427) | Not suitable | | 136 | [GSE55468](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE55468) | Genome-wide analysis of gene expression variation in CD4+ T cells from patients with active rheumatoid arthritis (RA). | none | Unclear study design | Tissue | suitability 0; metadata 78; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE55468) | Not suitable | ## Ranking explanations ### GSE101193 Dataset can inform exploration but is not strong enough for primary analysis. - Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 20%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 3 publications; 3 DOIs available: PMID 29140972, PMID 36405992, PMID 36940554. - Publication context: Long noncoding RNA profiling revealed differentially expressed lncRNAs associated with disease activity in PBMCs from patients with rheumatoid arthritis.. PloS one, 2017. PMID 29140972. DOI 10.1371/journal.pone.0186795. - Publication context: ST3GAL3 Promotes the Inflammatory Response of Fibroblast-Like Synoviocytes in Rheumatoid Arthritis by Activating the TLR9/MyD88 Pathway.. Mediators of inflammation, 2022. PMID 36405992. DOI 10.1155/2022/4258742. - Publication context: Identification and preliminary validation of synovial tissue-specific genes and their-mediated biological mechanisms in rheumatoid arthritis.. International immunopharmacology, 2023. PMID 36940554. DOI 10.1016/j.intimp.2023.109997. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs healthy control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Control type metadata detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than ten samples limit cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence. - RECOMMENDATION_REASON: Exploratory only: Dataset can inform exploration but is not strong enough for primary analysis. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE169082 Dataset can inform exploration but is not strong enough for primary analysis. - Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 20%. - Downgraded for tissue search because it is a biofluid cohort. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 3 publications; 3 DOIs available: PMID 34184082, PMID 39969652, PMID 40778323. - Publication context: circPTPN22 as a novel biomarker and ceRNA in peripheral blood mononuclear cells of rheumatoid arthritis.. Molecular medicine reports, 2021. PMID 34184082. DOI 10.3892/mmr.2021.12256. - Publication context: Integrative analysis of lncRNAs in rheumatoid arthritis: from bioinformatics to experimental validation.. Clinical and experimental medicine, 2025. PMID 39969652. DOI 10.1007/s10238-025-01589-z. - Publication context: Molecular profiling of rheumatoid Arthritis: Expression dynamics of hsa_circ_0092125 and G6PD in an integrative gene expression study.. Biochemistry and biophysics reports, 2025. PMID 40778323. DOI 10.1016/j.bbrep.2025.102180. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs healthy control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Control type metadata detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than ten samples limit cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence. - RECOMMENDATION_REASON: Exploratory only: Dataset can inform exploration but is not strong enough for primary analysis. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. - SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: ### GSE294225 Dataset can inform exploration but is not strong enough for primary analysis. - Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 20%. - Downgraded for tissue search because it is a biofluid cohort. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 40350372. - Publication context: Investigating endogenous immune-mediated monocyte memory in rheumatoid arthritis.. Annals of the rheumatic diseases, 2025. PMID 40350372. DOI 10.1016/j.ard.2025.03.016. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs healthy control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Control type metadata detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Exploratory only: Dataset can inform exploration but is not strong enough for primary analysis. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. ### GSE93272 Dataset can inform exploration but is not strong enough for primary analysis. - Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 20%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 21 publications; 20 DOIs available: PMID 30013029, PMID 36532040, PMID 36717858, PMID 36891318, PMID 37008939. - Publication context: Multi-omics monitoring of drug response in rheumatoid arthritis in pursuit of molecular remission.. Nature communications, 2018. PMID 30013029. DOI 10.1038/s41467-018-05044-4. - Publication context: SARS-CoV-2 induces "cytokine storm" hyperinflammatory responses in RA patients through pyroptosis.. Frontiers in immunology, 2022. PMID 36532040. DOI 10.3389/fimmu.2022.1058884. - Publication context: Identification of ferroptosis related markers by integrated bioinformatics analysis and In vitro model experiments in rheumatoid arthritis.. BMC medical genomics, 2023. PMID 36717858. DOI 10.1186/s12920-023-01445-7. - Publication context: 18 additional linked PubMed publications are available. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs healthy control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Control type metadata detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Exploratory only: Dataset can inform exploration but is not strong enough for primary analysis. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE110169 Dataset can inform exploration but is not strong enough for primary analysis. - Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 10%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis, Systemic lupus erythematosus. - Processed data is available for downstream review. - External evidence: PubMed links 5 publications; 5 DOIs available: PMID 29534336, PMID 40109657, PMID 41196273, PMID 42003657, PMID 42286429. - Publication context: Development of a Molecular Signature to Monitor Pharmacodynamic Responses Mediated by In Vivo Administration of Glucocorticoids.. Arthritis & rheumatology (Hoboken, N.J.), 2018. PMID 29534336. DOI 10.1002/art.40476. - Publication context: Identification of RSAD2 as a Key Biomarker Linking Iron Metabolism and Dendritic Cell Activation in Systemic Lupus Erythematosus Through Bioinformatics and Experimental Validation.. Journal of inflammation research, 2025. PMID 40109657. DOI 10.2147/JIR.S500115. - Publication context: Exploring the comorbidity mechanism of rheumatoid arthritis and systemic lupus erythematosus through transcriptomics and conducting experimental validation.. Clinical and experimental rheumatology, 2026. PMID 41196273. DOI 10.55563/clinexprheumatol/1xlydo. - Publication context: 2 additional linked PubMed publications are available. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs healthy control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Exploratory only: Dataset can inform exploration but is not strong enough for primary analysis. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE17755 Dataset can inform exploration but is not strong enough for primary analysis. - Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 10%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Lupus erythematosus, Rheumatoid arthritis, Systemic lupus erythematosus. - Processed data is available for downstream review. - External evidence: PubMed links 15 publications; 15 DOIs available: PMID 21496236, PMID 28316886, PMID 33430905, PMID 35789606, PMID 36189314. - Publication context: Underexpression of mitochondrial-DNA encoded ATP synthesis-related genes and DNA repair genes in systemic lupus erythematosus.. Arthritis research & therapy, 2011. PMID 21496236. DOI 10.1186/ar3317. - Publication context: Identification of dysregulated genes in rheumatoid arthritis based on bioinformatics analysis.. PeerJ, 2017. PMID 28316886. DOI 10.7717/peerj.3078. - Publication context: A 9 mRNAs-based diagnostic signature for rheumatoid arthritis by integrating bioinformatic analysis and machine-learning.. Journal of orthopaedic surgery and research, 2021. PMID 33430905. DOI 10.1186/s13018-020-02180-w. - Publication context: 12 additional linked PubMed publications are available. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs healthy control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Exploratory only: Dataset can inform exploration but is not strong enough for primary analysis. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE10500 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 5 publications; 4 DOIs available: PMID 18345002, PMID 34764682, PMID 37573587, PMID 39466354, PMID 40859359. - Publication context: TNF activates an IRF1-dependent autocrine loop leading to sustained expression of chemokines and STAT1-dependent type I interferon-response genes.. Nature immunology, 2008. PMID 18345002. DOI 10.1038/ni1576. - Publication context: Identification of Candidate Genes Related to Synovial Macrophages in Rheumatoid Arthritis by Bioinformatics Analysis.. International journal of general medicine, 2021. PMID 34764682. DOI 10.2147/IJGM.S333512. - Publication context: Dissecting the Imbalance of Synovial Macrophages in Rheumatoid Arthritis.. Alternative therapies in health and medicine, 2023. PMID 37573587. - Publication context: 2 additional linked PubMed publications are available. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs normal tissue. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than ten samples limit cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE111946 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Tissue. Comparison suitability: 0%. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 30157923. - Publication context: Osteogenic differentiation of fibroblast-like synovial cells in rheumatoid arthritis is induced by microRNA-218 through a ROBO/Slit pathway.. Arthritis research & therapy, 2018. PMID 30157923. DOI 10.1186/s13075-018-1703-z. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs genetic control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Control type metadata detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - COMPARISON_SUITABILITY: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking. - DOWNGRADE_REASON: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than six samples are too small for top-ranked cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than six samples are too small for top-ranked cohort confidence. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: SMALL_COHORT_NEEDS_REVIEW [warning]: Dataset has fewer than six samples and should not be treated as a high-confidence cohort without manual review. - WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - SMALL_COHORT_NEEDS_REVIEW [WARNING]: Dataset has fewer than six samples and should not be treated as a high-confidence cohort without manual review.; samples: - SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE12021 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Tissue. Comparison suitability: 0%. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 21 publications; 21 DOIs available: PMID 18721452, PMID 39534605, PMID 39616227, PMID 40059948, PMID 40083558. - Publication context: Identification of intra-group, inter-individual, and gene-specific variances in mRNA expression profiles in the rheumatoid arthritis synovial membrane.. Arthritis research & therapy, 2008. PMID 18721452. DOI 10.1186/ar2485. - Publication context: YTHDC1 Regulates the Migration, Invasion, Proliferation, and Apoptosis of Rheumatoid Fibroblast-Like Synoviocytes.. Frontiers in immunology, 2024. PMID 39534605. DOI 10.3389/fimmu.2024.1440398. - Publication context: Kaempferol alleviates rheumatoid arthritis through pyroptosis based on bioinformatics analysis and experimental validation.. Scientific reports, 2024. PMID 39616227. DOI 10.1038/s41598-024-81833-w. - Publication context: 18 additional linked PubMed publications are available. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs healthy control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Control type metadata detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE121894 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 34432202, PMID 37926093. - Publication context: Inokosterone Is A Potential Drug Target of Estrogen Receptor 1 in Rheumatoid Arthritis Patients: Analysis from Active Ingredient of Cyathula Officinalis.. Chinese journal of integrative medicine, 2021. PMID 34432202. DOI 10.1007/s11655-021-3492-5. - Publication context: Bone Marrow Mesenchymal Stem Cells Release miR-378a-5p-Carried Extracellular Vesicles to Alleviate Rheumatoid Arthritis.. Journal of innate immunity, 2023. PMID 37926093. DOI 10.1159/000534830. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs mixed controls. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Control type metadata detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE128813 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Cell line. Comparison suitability: 0%. - Downgraded for tissue search because it is a model-system experiment. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 3 publications; 3 DOIs available: PMID 31791845, PMID 37814309, PMID 39433011. - Publication context: LncRNA PICSAR promotes cell proliferation, migration and invasion of fibroblast-like synoviocytes by sponging miRNA-4701-5p in rheumatoid arthritis.. EBioMedicine, 2019. PMID 31791845. DOI 10.1016/j.ebiom.2019.11.024. - Publication context: Identification of the potential regulatory interactions in rheumatoid arthritis through a comprehensive analysis of lncRNA-related ceRNA networks.. BMC musculoskeletal disorders, 2023. PMID 37814309. DOI 10.1186/s12891-023-06936-3. - Publication context: Identification of serum exosomal lncRNAs and their potential regulation of characteristic genes of fibroblast-like synoviocytes in rheumatoid arthritis.. International immunopharmacology, 2024. PMID 39433011. DOI 10.1016/j.intimp.2024.113382. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs healthy control. - COMPARISON_SUITABILITY: Excluded sample type flags reduce suitability. - DOWNGRADE_REASON: Excluded sample type flags reduce suitability. - COMPARISON_SUITABILITY: Control type metadata detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - COMPARISON_SUITABILITY: Organoid or cell-line experiment downgraded for patient tissue search intent. - DOWNGRADE_REASON: Organoid or cell-line experiment downgraded for patient tissue search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - COMPARISON_SUITABILITY: Excluded model-system sample markers reduce suitability. - DOWNGRADE_REASON: Excluded model-system sample markers reduce suitability. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than ten samples limit cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded for tissue search because it is a model-system experiment. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MIXED_SAMPLE_TYPES [warning]: Multiple sample type labels or exclusion flags were detected. - WARNING_CODE: CELL_LINES_INCLUDED [warning]: Cell line samples appear to be included. - WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - MIXED_SAMPLE_TYPES [WARNING]: Multiple sample type labels or exclusion flags were detected.; samples: - CELL_LINES_INCLUDED [WARNING]: Cell line samples appear to be included.; samples: GSM3685848, GSM3685849, GSM3685850, GSM3685851, GSM3685852, GSM3685853 - SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE13026 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 19563633. - Publication context: Early and long-standing rheumatoid arthritis: distinct molecular signatures identified by gene-expression profiling in synovia.. Arthritis research & therapy, 2009. PMID 19563633. DOI 10.1186/ar2744. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE133426 Dataset does not meet the current suitability threshold. - Comparison: Treatment vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because it is a treatment/control experiment. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 31379807. - Publication context: Human Memory Th17 Cell Populations Change Into Anti-inflammatory Cells With Regulatory Capacity Upon Exposure to Active Vitamin D.. Frontiers in immunology, 2019. PMID 31379807. DOI 10.3389/fimmu.2019.01504. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Treated and untreated sample groups detected. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Control type metadata detected. - COMPARISON_SUITABILITY: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - DOWNGRADE_REASON: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than ten samples limit cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Treatment vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because it is a treatment/control experiment. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE134087 Dataset does not meet the current suitability threshold. - Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 32509015, PMID 36940554. - Publication context: Differential long non-coding RNA expression profiles in the peripheral blood and CD4(+) T cells of patients with active rheumatoid arthritis.. Experimental and therapeutic medicine, 2020. PMID 32509015. DOI 10.3892/etm.2020.8681. - Publication context: Identification and preliminary validation of synovial tissue-specific genes and their-mediated biological mechanisms in rheumatoid arthritis.. International immunopharmacology, 2023. PMID 36940554. DOI 10.1016/j.intimp.2023.109997. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs healthy control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Control type metadata detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than six samples are too small for top-ranked cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than six samples are too small for top-ranked cohort confidence. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: SMALL_COHORT_NEEDS_REVIEW [warning]: Dataset has fewer than six samples and should not be treated as a high-confidence cohort without manual review. - WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - SMALL_COHORT_NEEDS_REVIEW [WARNING]: Dataset has fewer than six samples and should not be treated as a high-confidence cohort without manual review.; samples: - SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE1402 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: Expression Atlas curated experiment link is available. - External evidence: PubMed links 3 publications; 3 DOIs available: PMID 15150433, PMID 35967305, PMID 39699225. - Publication context: Gene expression in juvenile arthritis and spondyloarthropathy: pro-angiogenic ELR+ chemokine genes relate to course of arthritis.. Rheumatology (Oxford, England), 2004. PMID 15150433. DOI 10.1093/rheumatology/keh224. - Publication context: A Cross-Tissue Transcriptome-Wide Association Study Identifies Novel Susceptibility Genes for Juvenile Idiopathic Arthritis in Asia and Europe.. Frontiers in immunology, 2022. PMID 35967305. DOI 10.3389/fimmu.2022.941398. - Publication context: Identification and validation of susceptibility modules and hub genes in polyarticular juvenile idiopathic arthritis using WGCNA and machine learning.. Autoimmunity, 2025. PMID 39699225. DOI 10.1080/08916934.2024.2437239. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE141934 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 31945409. - Publication context: Lymphocyte DNA methylation mediates genetic risk at shared immune-mediated disease loci.. The Journal of allergy and clinical immunology, 2020. PMID 31945409. DOI 10.1016/j.jaci.2019.12.910. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Non-RNA-seq assay context downgraded for RNA-seq dataset discovery. - DOWNGRADE_REASON: Non-RNA-seq assay context downgraded for RNA-seq dataset discovery. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because the assay context is not primary RNA-seq expression profiling. - DOWNGRADE_REASON: Overall score capped because the assay context is not primary RNA-seq expression profiling. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: THIRD_PARTY_REANALYSIS [warning]: This record is a third-party integration or reanalysis of public datasets. The GEO sample count may describe deposited atlas records rather than one independent clinical cohort; verify source-study provenance before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - THIRD_PARTY_REANALYSIS [WARNING]: This record is a third-party integration or reanalysis of public datasets. The GEO sample count may describe deposited atlas records rather than one independent clinical cohort; verify source-study provenance before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE142049 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Lupus erythematosus, Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 31945409. - Publication context: Lymphocyte DNA methylation mediates genetic risk at shared immune-mediated disease loci.. The Journal of allergy and clinical immunology, 2020. PMID 31945409. DOI 10.1016/j.jaci.2019.12.910. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Non-RNA-seq assay context downgraded for RNA-seq dataset discovery. - DOWNGRADE_REASON: Non-RNA-seq assay context downgraded for RNA-seq dataset discovery. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because the assay context is not primary RNA-seq expression profiling. - DOWNGRADE_REASON: Overall score capped because the assay context is not primary RNA-seq expression profiling. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: THIRD_PARTY_REANALYSIS [warning]: This record is a third-party integration or reanalysis of public datasets. The GEO sample count may describe deposited atlas records rather than one independent clinical cohort; verify source-study provenance before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - THIRD_PARTY_REANALYSIS [WARNING]: This record is a third-party integration or reanalysis of public datasets. The GEO sample count may describe deposited atlas records rather than one independent clinical cohort; verify source-study provenance before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE142607 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Tissue. Comparison suitability: 0%. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 33256735. - Publication context: Reprogramming of synovial macrophage metabolism by synovial fibroblasts under inflammatory conditions.. Cell communication and signaling : CCS, 2020. PMID 33256735. DOI 10.1186/s12964-020-00678-8. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs healthy control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because non-human datasets are outside the selected human ranking intent. - DOWNGRADE_REASON: Overall score capped because non-human datasets are outside the selected human ranking intent. - OVERALL: Overall score capped because fewer than ten samples limit cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - WARNING_CODE: INTENT_ASSAY_MISMATCH [critical]: Dataset organism does not match the human patient-tissue tumor-normal intent. - INTENT_ASSAY_MISMATCH [CRITICAL]: Dataset organism does not match the human patient-tissue tumor-normal intent.; samples: ### GSE148395 Dataset does not meet the current suitability threshold. - Comparison: Treatment vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because it is a treatment/control experiment. - Downgraded for tissue search because study design or specimen source is unclear. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 33288543. - Publication context: Integration of the Transcriptome and Genome-Wide Landscape of BRD2 and BRD4 Binding Motifs Identifies Key Superenhancer Genes and Reveals the Mechanism of Bet Inhibitor Action in Rheumatoid Arthritis Synovial Fibroblasts.. Journal of immunology (Baltimore, Md. : 1950), 2021. PMID 33288543. DOI 10.4049/jimmunol.2000286. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Treated and untreated sample groups detected. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Control type metadata detected. - COMPARISON_SUITABILITY: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - DOWNGRADE_REASON: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Treatment vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because it is a treatment/control experiment. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE153378 Dataset does not meet the current suitability threshold. - Comparison: Treatment vs control. Specimen: Tissue. Comparison suitability: 0%. - Downgraded for tissue search because it is a treatment/control experiment. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 34345282. - Publication context: Expression profiling of genes in rheumatoid fibroblast-like synoviocytes regulated by Fas ligand via cDNA microarray analysis.. Experimental and therapeutic medicine, 2021. PMID 34345282. DOI 10.3892/etm.2021.10432. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - DOWNGRADE_REASON: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than ten samples limit cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded for tissue search because it is a treatment/control experiment. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - TREATED_SAMPLES_NEED_REVIEW [INFO]: Treated samples may need review depending on the comparison.; samples: GSM4643212, GSM4643214, GSM4643216, GSM4643218 - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE15573 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 9 publications; 9 DOIs available: PMID 19710928, PMID 28818099, PMID 35589811, PMID 37595490, PMID 39466354. - Publication context: Transcriptome analysis describing new immunity and defense genes in peripheral blood mononuclear cells of rheumatoid arthritis patients.. PloS one, 2009. PMID 19710928. DOI 10.1371/journal.pone.0006803. - Publication context: Biosemantics guided gene expression profiling of Sjögren's syndrome: a comparative analysis with systemic lupus erythematosus and rheumatoid arthritis.. Arthritis research & therapy, 2017. PMID 28818099. DOI 10.1186/s13075-017-1400-3. - Publication context: PCBP1 is associated with rheumatoid arthritis by affecting RNA products of genes involved in immune response in Th1 cells.. Scientific reports, 2022. PMID 35589811. DOI 10.1038/s41598-022-12594-7. - Publication context: 6 additional linked PubMed publications are available. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE157047 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Mixed specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because specimen/source classes are mixed. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 36194479, PMID 37916875. - Publication context: NLRC4-mediated activation of CD1c+ DC contributes to perpetuation of synovitis in rheumatoid arthritis.. JCI insight, 2022. PMID 36194479. DOI 10.1172/jci.insight.152886. - Publication context: MICa/b-dependent activation of natural killer cells by CD64(+) inflammatory type 2 dendritic cells contributes to autoimmunity.. The EMBO journal, 2023. PMID 37916875. DOI 10.15252/embj.2023113714. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - COMPARISON_SUITABILITY: Mixed specimen/source dataset downgraded until tissue samples are clearly separated. - DOWNGRADE_REASON: Mixed specimen/source dataset downgraded until tissue samples are clearly separated. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded for tissue search because specimen/source classes are mixed. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE181614 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Tissue. Comparison suitability: 0%. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 36542956, PMID 39433011. - Publication context: LncRNA RNA XIST binding to GATA1 contributes to rheumatoid arthritis through its effects on proliferation of synovial fibroblasts and angiogenesis via regulation of CCN6.. Molecular immunology, 2023. PMID 36542956. DOI 10.1016/j.molimm.2022.12.004. - Publication context: Identification of serum exosomal lncRNAs and their potential regulation of characteristic genes of fibroblast-like synoviocytes in rheumatoid arthritis.. International immunopharmacology, 2024. PMID 39433011. DOI 10.1016/j.intimp.2024.113382. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE189136 Dataset does not meet the current suitability threshold. - Comparison: Treatment vs control. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded for tissue search because it is a treatment/control experiment. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 35002734. - Publication context: Targeting MyD88 Downregulates Inflammatory Mediators and Pathogenic Processes in PBMC From DMARDs-Naïve Rheumatoid Arthritis Patients.. Frontiers in pharmacology, 2021. PMID 35002734. DOI 10.3389/fphar.2021.800220. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Treated and untreated sample groups detected. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - DOWNGRADE_REASON: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded for tissue search because it is a treatment/control experiment. ### GSE189338 Dataset does not meet the current suitability threshold. - Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Lupus erythematosus, Rheumatoid arthritis, Systemic lupus erythematosus. - Processed data is available for downstream review. - External evidence: PubMed links 3 publications; 3 DOIs available: PMID 35379246, PMID 40778323, PMID 42246038. - Publication context: Expression profile of circRNA in peripheral blood mononuclear cells of patients with rheumatoid arthritis.. BMC medical genomics, 2022. PMID 35379246. DOI 10.1186/s12920-022-01225-9. - Publication context: Molecular profiling of rheumatoid Arthritis: Expression dynamics of hsa_circ_0092125 and G6PD in an integrative gene expression study.. Biochemistry and biophysics reports, 2025. PMID 40778323. DOI 10.1016/j.bbrep.2025.102180. - Publication context: Construction and Analysis of ceRNA Regulatory Networks Reveal the Core Genes Associated with Rheumatoid Arthritis.. International journal of general medicine, 2026. PMID 42246038. DOI 10.2147/IJGM.S589139. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs healthy control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - COMPARISON_SUITABILITY: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking. - DOWNGRADE_REASON: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than ten samples limit cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE1919 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: Expression Atlas curated experiment link is available. - External evidence: PubMed links 21 publications; 21 DOIs available: PMID 20858714, PMID 36389761, PMID 36459007, PMID 36468029, PMID 36681837. - Publication context: Molecular signatures and new candidates to target the pathogenesis of rheumatoid arthritis.. Physiological genomics, 2010. PMID 20858714. DOI 10.1152/physiolgenomics.00004.2010. - Publication context: Exploring the molecular mechanisms and shared gene signatures between rheumatoid arthritis and diffuse large B cell lymphoma.. Frontiers in immunology, 2022. PMID 36389761. DOI 10.3389/fimmu.2022.1036239. - Publication context: Screening and validation for core genes in osteoarthritic cartilage based on weighted gene co-expression network analysis.. European review for medical and pharmacological sciences, 2022. PMID 36459007. DOI 10.26355/eurrev_202211_30355. - Publication context: 18 additional linked PubMed publications are available. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs normal tissue. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE195557 Dataset does not meet the current suitability threshold. - Comparison: Treatment vs control. Specimen: Tissue. Comparison suitability: 0%. - Downgraded for tissue search because it is a treatment/control experiment. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 35258553. - Publication context: TNFR2 is critical for TNF-induced rheumatoid arthritis fibroblast-like synoviocyte inflammation.. Rheumatology (Oxford, England), 2022. PMID 35258553. DOI 10.1093/rheumatology/keac124. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Knockdown and control sample groups detected. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Control type metadata detected. - COMPARISON_SUITABILITY: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - DOWNGRADE_REASON: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded for tissue search because it is a treatment/control experiment. ### GSE197057 Dataset does not meet the current suitability threshold. - Comparison: Treatment vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because it is a treatment/control experiment. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 38401037. - Publication context: LIGHT regulated gene expression in rheumatoid synovial fibroblasts.. Molecular biology reports, 2024. PMID 38401037. DOI 10.1007/s11033-024-09311-0. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - DOWNGRADE_REASON: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than ten samples limit cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Treatment vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because it is a treatment/control experiment. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - TREATED_SAMPLES_NEED_REVIEW [INFO]: Treated samples may need review depending on the comparison.; samples: GSM5907682, GSM5907684, GSM5907686, GSM5907688 - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE200291 Dataset does not meet the current suitability threshold. - Comparison: Treatment vs control. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded for tissue search because it is a treatment/control experiment. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Treated and untreated sample groups detected. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - DOWNGRADE_REASON: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded for tissue search because it is a treatment/control experiment. - WARNING_CODE: TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison. - WARNING_CODE: TREATED_AND_UNTREATED_SAMPLES_MIXED [info]: Treated and untreated samples are both present. - TREATED_SAMPLES_NEED_REVIEW [INFO]: Treated samples may need review depending on the comparison.; samples: GSM6030350, GSM6030361, GSM6030372, GSM6030383, GSM6030394, GSM6030404, GSM6030415, GSM6030426, GSM6030437 - TREATED_AND_UNTREATED_SAMPLES_MIXED [INFO]: Treated and untreated samples are both present.; samples: ### GSE2053 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 3 publications; 3 DOIs available: PMID 20858714, PMID 24238402, PMID 42127012. - Publication context: Molecular signatures and new candidates to target the pathogenesis of rheumatoid arthritis.. Physiological genomics, 2010. PMID 20858714. DOI 10.1152/physiolgenomics.00004.2010. - Publication context: Bioinformatic analysis to find small molecules related to rheumatoid arthritis.. International journal of rheumatic diseases, 2014. PMID 24238402. DOI 10.1111/1756-185X.12201. - Publication context: KIF11 promotes rheumatoid arthritis pathogenesis by activating M1 macrophage polarization and promoting inflammatory cytokine secretion.. PloS one, 2026. PMID 42127012. DOI 10.1371/journal.pone.0347313. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs normal tissue. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than ten samples limit cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE205795 Dataset does not meet the current suitability threshold. - Comparison: Treatment vs control. Specimen: Tissue. Comparison suitability: 0%. - Downgraded for tissue search because it is a treatment/control experiment. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Treated and untreated sample groups detected. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Control type metadata detected. - COMPARISON_SUITABILITY: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - DOWNGRADE_REASON: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than ten samples limit cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded for tissue search because it is a treatment/control experiment. ### GSE205962 Dataset does not meet the current suitability threshold. - Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 4 publications; 4 DOIs available: PMID 37143094, PMID 39309832, PMID 40500570, PMID 40636547. - Publication context: Integrative network fusion-based multi-omics study for biomarker identification and patient classification of rheumatoid arthritis.. Chinese medicine, 2023. PMID 37143094. DOI 10.1186/s13020-023-00750-8. - Publication context: Combining bioinformatics, network pharmacology, and artificial intelligence to predict the mechanism of resveratrol in the treatment of rheumatoid arthritis.. Heliyon, 2024. PMID 39309832. DOI 10.1016/j.heliyon.2024.e37371. - Publication context: Machine learning and bioinformatics analysis to identify and validate diagnostic model associated with immune infiltration in rheumatoid arthritis.. Clinical rheumatology, 2025. PMID 40500570. DOI 10.1007/s10067-025-07514-9. - Publication context: 1 additional linked PubMed publications are available. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs healthy control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Control type metadata detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE206848 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Tissue. Comparison suitability: 0%. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 9 publications; 9 DOIs available: PMID 38770093, PMID 38814177, PMID 39313038, PMID 39466354, PMID 39587568. - Publication context: TPX2 upregulates MMP13 to promote the progression of lipopolysaccharide-induced osteoarthritis.. PeerJ, 2024. PMID 38770093. DOI 10.7717/peerj.17032. - Publication context: Machine learning-based identification and immune characterization of ferroptosis-related molecular clusters in osteoarthritis and validation.. Aging, 2024. PMID 38814177. DOI 10.18632/aging.205875. - Publication context: PU.1 regulates osteoarthritis progression via CSF1R in synovial cells.. Biochimica et biophysica acta. Molecular basis of disease, 2025. PMID 39313038. DOI 10.1016/j.bbadis.2024.167525. - Publication context: 6 additional linked PubMed publications are available. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs normal tissue. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE213842 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Tissue. Comparison suitability: 0%. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs healthy control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Control type metadata detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - COMPARISON_SUITABILITY: Non-RNA-seq assay context downgraded for RNA-seq dataset discovery. - DOWNGRADE_REASON: Non-RNA-seq assay context downgraded for RNA-seq dataset discovery. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than ten samples limit cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence. - OVERALL: Overall score capped because the assay context is not primary RNA-seq expression profiling. - DOWNGRADE_REASON: Overall score capped because the assay context is not primary RNA-seq expression profiling. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. ### GSE217012 Dataset does not meet the current suitability threshold. - Comparison: Treatment vs control. Specimen: Tissue. Comparison suitability: 0%. - Downgraded for tissue search because it is a treatment/control experiment. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 37749630, PMID 40447853. - Publication context: MyD88 dimerization inhibitor ST2825 targets the aggressiveness of synovial fibroblasts in rheumatoid arthritis patients.. Arthritis research & therapy, 2023. PMID 37749630. DOI 10.1186/s13075-023-03145-0. - Publication context: The distinct transcriptomic signature of the resolution phase fibroblast-like synoviocytes supports endothelial cell dysfunction.. Communications biology, 2025. PMID 40447853. DOI 10.1038/s42003-025-08250-1. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Treated and untreated sample groups detected. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - DOWNGRADE_REASON: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded for tissue search because it is a treatment/control experiment. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: ### GSE21959 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 5 publications; 5 DOIs available: PMID 20848564, PMID 26404854, PMID 28767591, PMID 35305721, PMID 36530571. - Publication context: The transcriptional response of normal and rheumatoid arthritis synovial fibroblasts to hypoxia.. Arthritis and rheumatism, 2010. PMID 20848564. DOI 10.1002/art.27750. - Publication context: Analysis of differences in the molecular mechanism of rheumatoid arthritis and osteoarthritis based on integration of gene expression profiles.. Immunology letters, 2015. PMID 26404854. DOI 10.1016/j.imlet.2015.09.011. - Publication context: Identification of key genes associated with rheumatoid arthritis with bioinformatics approach.. Medicine, 2017. PMID 28767591. DOI 10.1097/MD.0000000000007673. - Publication context: 2 additional linked PubMed publications are available. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs healthy control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Control type metadata detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE23561 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Metabolic disease, Rheumatoid arthritis, Type 2 diabetes. - Processed data is available for downstream review. - External evidence: PubMed links 15 publications; 15 DOIs available: PMID 21368773, PMID 26944061, PMID 28595632, PMID 33052139, PMID 34697898. - Publication context: Peripheral blood gene expression profiles in metabolic syndrome, coronary artery disease and type 2 diabetes.. Genes and immunity, 2011. PMID 21368773. DOI 10.1038/gene.2011.13. - Publication context: Weighted gene co-expression network analysis identifies specific modules and hub genes related to coronary artery disease.. BMC cardiovascular disorders, 2016. PMID 26944061. DOI 10.1186/s12872-016-0217-3. - Publication context: A comparison of gene expression profiles in patients with coronary artery disease, type 2 diabetes, and their coexisting conditions.. Diagnostic pathology, 2017. PMID 28595632. DOI 10.1186/s13000-017-0630-7. - Publication context: 12 additional linked PubMed publications are available. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE236924 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Tissue. Comparison suitability: 0%. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Inflammatory bowel disease, Rheumatoid arthritis, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 3 publications; 3 DOIs available: PMID 37490914, PMID 39466354, PMID 40287562. - Publication context: An agonistic anti-signal regulatory protein α antibody for chronic inflammatory diseases.. Cell reports. Medicine, 2023. PMID 37490914. DOI 10.1016/j.xcrm.2023.101130. - Publication context: Identification and Experimental Verification of PDK4 as a Potential Biomarker for Diagnosis and Treatment in Rheumatoid Arthritis.. Molecular biotechnology, 2025. PMID 39466354. DOI 10.1007/s12033-024-01297-1. - Publication context: SLAM receptors regulate immune checkpoints via SAP and EAT- 2 in rheumatoid arthritis: association with disease activity.. Clinical rheumatology, 2025. PMID 40287562. DOI 10.1007/s10067-025-07461-5. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: oa vs control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE24742 Dataset does not meet the current suitability threshold. - Comparison: Treatment vs control. Specimen: Biopsy. Comparison suitability: 0%. - Downgraded for tissue search because it is a treatment/control experiment. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 21337318, PMID 25927832. - Publication context: Rituximab treatment induces the expression of genes involved in healing processes in the rheumatoid arthritis synovium.. Arthritis and rheumatism, 2011. PMID 21337318. DOI 10.1002/art.30292. - Publication context: Heterogeneity of synovial molecular patterns in patients with arthritis.. PloS one, 2015. PMID 25927832. DOI 10.1371/journal.pone.0122104. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Treated and untreated sample groups detected. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - DOWNGRADE_REASON: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded for tissue search because it is a treatment/control experiment. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison. - WARNING_CODE: TREATED_AND_UNTREATED_SAMPLES_MIXED [info]: Treated and untreated samples are both present. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - TREATED_SAMPLES_NEED_REVIEW [INFO]: Treated samples may need review depending on the comparison.; samples: GSM607508, GSM607509, GSM609031, GSM609032, GSM609033, GSM609034, GSM609035, GSM609036, GSM609038, GSM609386, GSM609387, GSM609388, GSM609389, GSM609390, GSM609391, GSM609392, GSM609393, GSM609394, GSM609395, GSM609396, GSM609397, GSM609398, GSM609399 - TREATED_AND_UNTREATED_SAMPLES_MIXED [INFO]: Treated and untreated samples are both present.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE290552 Dataset does not meet the current suitability threshold. - Comparison: Treatment vs control. Specimen: Cell line. Comparison suitability: 0%. - Downgraded for tissue search because it is a model-system experiment. - Downgraded for tissue search because it is a treatment/control experiment. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Infectious disease or host response, Neurodegeneration, Pancreatic cancer, Prostate cancer, Rheumatoid arthritis, Sepsis. - Processed data is available for downstream review. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: stimulated vs control. - COMPARISON_SUITABILITY: Excluded sample type flags reduce suitability. - DOWNGRADE_REASON: Excluded sample type flags reduce suitability. - COMPARISON_SUITABILITY: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - DOWNGRADE_REASON: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - COMPARISON_SUITABILITY: Organoid or cell-line experiment downgraded for patient tissue search intent. - DOWNGRADE_REASON: Organoid or cell-line experiment downgraded for patient tissue search intent. - COMPARISON_SUITABILITY: Excluded model-system sample markers reduce suitability. - DOWNGRADE_REASON: Excluded model-system sample markers reduce suitability. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded for tissue search because it is a model-system experiment. - DOWNGRADE_REASON: Downgraded for tissue search because it is a treatment/control experiment. - WARNING_CODE: MIXED_SAMPLE_TYPES [warning]: Multiple sample type labels or exclusion flags were detected. - WARNING_CODE: CELL_LINES_INCLUDED [warning]: Cell line samples appear to be included. - WARNING_CODE: TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison. - MIXED_SAMPLE_TYPES [WARNING]: Multiple sample type labels or exclusion flags were detected.; samples: - CELL_LINES_INCLUDED [WARNING]: Cell line samples appear to be included.; samples: GSM8816432, GSM8816433, GSM8816434, GSM8816435, GSM8816436, GSM8816437, GSM8816438, GSM8816439, GSM8816440, GSM8816441, GSM8816442, GSM8816443, GSM8816444, GSM8816445, GSM8816446, GSM8816447 - TREATED_SAMPLES_NEED_REVIEW [INFO]: Treated samples may need review depending on the comparison.; samples: GSM8816432, GSM8816433, GSM8816434, GSM8816435, GSM8816436, GSM8816437, GSM8816438, GSM8816439, GSM8816440, GSM8816441, GSM8816442, GSM8816443, GSM8816444, GSM8816445, GSM8816446, GSM8816447 ### GSE29746 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 11 publications; 11 DOIs available: PMID 22021863, PMID 27082252, PMID 35461155, PMID 36995411, PMID 38020130. - Publication context: Transcriptome analysis reveals specific changes in osteoarthritis synovial fibroblasts.. Annals of the rheumatic diseases, 2012. PMID 22021863. DOI 10.1136/annrheumdis-2011-200281. - Publication context: Comparison of molecular mechanisms of rheumatoid arthritis and osteoarthritis using gene microarrays.. Molecular medicine reports, 2016. PMID 27082252. DOI 10.3892/mmr.2016.5144. - Publication context: Monoamine oxidase A attenuates chondrocyte loss and extracellular matrix degradation in osteoarthritis by inducing autophagy.. International immunopharmacology, 2022. PMID 35461155. DOI 10.1016/j.intimp.2022.108772. - Publication context: 8 additional linked PubMed publications are available. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs healthy control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE301891 Dataset does not meet the current suitability threshold. - Comparison: Treatment vs control. Specimen: Cell line. Comparison suitability: 0%. - Downgraded for tissue search because it is a model-system experiment. - Downgraded for tissue search because it is a treatment/control experiment. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: treated vs control. - COMPARISON_SUITABILITY: Excluded sample type flags reduce suitability. - DOWNGRADE_REASON: Excluded sample type flags reduce suitability. - COMPARISON_SUITABILITY: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - DOWNGRADE_REASON: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - COMPARISON_SUITABILITY: Organoid or cell-line experiment downgraded for patient tissue search intent. - DOWNGRADE_REASON: Organoid or cell-line experiment downgraded for patient tissue search intent. - COMPARISON_SUITABILITY: Excluded model-system sample markers reduce suitability. - DOWNGRADE_REASON: Excluded model-system sample markers reduce suitability. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than ten samples limit cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded for tissue search because it is a model-system experiment. - DOWNGRADE_REASON: Downgraded for tissue search because it is a treatment/control experiment. - WARNING_CODE: MIXED_SAMPLE_TYPES [warning]: Multiple sample type labels or exclusion flags were detected. - WARNING_CODE: CELL_LINES_INCLUDED [warning]: Cell line samples appear to be included. - MIXED_SAMPLE_TYPES [WARNING]: Multiple sample type labels or exclusion flags were detected.; samples: - CELL_LINES_INCLUDED [WARNING]: Cell line samples appear to be included.; samples: GSM9091598, GSM9091599, GSM9091600, GSM9091601, GSM9091602, GSM9091603 ### GSE34391 Dataset does not meet the current suitability threshold. - Comparison: Treatment vs control. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded for tissue search because it is a treatment/control experiment. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Lupus erythematosus, Rheumatoid arthritis. - Processed data is available for downstream review. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: lupus erythematosus vs healthy control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Control type metadata detected. - COMPARISON_SUITABILITY: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - DOWNGRADE_REASON: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - COMPARISON_SUITABILITY: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking. - DOWNGRADE_REASON: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than six samples are too small for top-ranked cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than six samples are too small for top-ranked cohort confidence. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded for tissue search because it is a treatment/control experiment. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison. - WARNING_CODE: SAMPLE_COUNT_BELOW_THRESHOLD [warning]: Total sample count is below the minimum needed for two comparison groups. - WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - TREATED_SAMPLES_NEED_REVIEW [INFO]: Treated samples may need review depending on the comparison.; samples: GSM848179, GSM848180 - SAMPLE_COUNT_BELOW_THRESHOLD [WARNING]: Total sample count is below the minimum needed for two comparison groups.; samples: - SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE4255 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Tissue. Comparison suitability: 0%. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 16638801. - Publication context: A genome-scale assessment of peripheral blood B-cell molecular homeostasis in patients with rheumatoid arthritis.. Rheumatology (Oxford, England), 2006. PMID 16638801. DOI 10.1093/rheumatology/kel095. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than six samples are too small for top-ranked cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than six samples are too small for top-ranked cohort confidence. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: SAMPLE_COUNT_BELOW_THRESHOLD [warning]: Total sample count is below the minimum needed for two comparison groups. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - SAMPLE_COUNT_BELOW_THRESHOLD [WARNING]: Total sample count is below the minimum needed for two comparison groups.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE45867 Dataset does not meet the current suitability threshold. - Comparison: Treatment vs control. Specimen: Tissue. Comparison suitability: 0%. - Downgraded for tissue search because it is a treatment/control experiment. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 24449571, PMID 25927832. - Publication context: Global molecular effects of tocilizumab therapy in rheumatoid arthritis synovium.. Arthritis & rheumatology (Hoboken, N.J.), 2014. PMID 24449571. DOI 10.1002/art.38202. - Publication context: Heterogeneity of synovial molecular patterns in patients with arthritis.. PloS one, 2015. PMID 25927832. DOI 10.1371/journal.pone.0122104. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Treated and untreated sample groups detected. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - DOWNGRADE_REASON: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded for tissue search because it is a treatment/control experiment. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison. - WARNING_CODE: TREATED_AND_UNTREATED_SAMPLES_MIXED [info]: Treated and untreated samples are both present. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - TREATED_SAMPLES_NEED_REVIEW [INFO]: Treated samples may need review depending on the comparison.; samples: GSM1116934, GSM1116936, GSM1116938, GSM1116940, GSM1116942, GSM1116944, GSM1116946, GSM1116948, GSM1116950, GSM1116952, GSM1116954, GSM1116956, GSM1116958, GSM1116960, GSM1116962, GSM1116964, GSM1116966, GSM1116968, GSM1116970, GSM1116972 - TREATED_AND_UNTREATED_SAMPLES_MIXED [INFO]: Treated and untreated samples are both present.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE55235 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Tissue. Comparison suitability: 0%. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: Expression Atlas curated experiment link is available. - External evidence: PubMed links 21 publications; 21 DOIs available: PMID 24690414, PMID 40885352, PMID 40958328, PMID 41007174, PMID 41209768. - Publication context: Identification of rheumatoid arthritis and osteoarthritis patients by transcriptome-based rule set generation.. Arthritis research & therapy, 2014. PMID 24690414. DOI 10.1186/ar4526. - Publication context: G protein-coupled receptor-related genes matrix metallopeptidase 9 and tachykinin precursor 1 promote osteoarthritis progression and influence the immune microenvironment.. International journal of biological macromolecules, 2025. PMID 40885352. DOI 10.1016/j.ijbiomac.2025.147208. - Publication context: Elucidation of hub cross-talk genes as potential biomarkers and drug prediction for chronic periodontitis and rheumatoid arthritis: A bioinformatics analysis.. Medicine, 2025. PMID 40958328. DOI 10.1097/MD.0000000000044358. - Publication context: 18 additional linked PubMed publications are available. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: osteoarthritis vs healthy control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Control type metadata detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE55457 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Tissue. Comparison suitability: 0%. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 21 publications; 21 DOIs available: PMID 24690414, PMID 40765736, PMID 40885352, PMID 40958328, PMID 41007174. - Publication context: Identification of rheumatoid arthritis and osteoarthritis patients by transcriptome-based rule set generation.. Arthritis research & therapy, 2014. PMID 24690414. DOI 10.1186/ar4526. - Publication context: Integrated Bioinformatics and Experimental Validation Reveal Macrophage Polarization-Related Biomarkers for Osteoarthritis Diagnosis.. Journal of multidisciplinary healthcare, 2025. PMID 40765736. DOI 10.2147/JMDH.S537507. - Publication context: G protein-coupled receptor-related genes matrix metallopeptidase 9 and tachykinin precursor 1 promote osteoarthritis progression and influence the immune microenvironment.. International journal of biological macromolecules, 2025. PMID 40885352. DOI 10.1016/j.ijbiomac.2025.147208. - Publication context: 18 additional linked PubMed publications are available. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs healthy control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Control type metadata detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE56649 Dataset does not meet the current suitability threshold. - Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 25880754. - Publication context: CD4 T-cell transcriptome analysis reveals aberrant regulation of STAT3 and Wnt signaling pathways in rheumatoid arthritis: evidence from a case-control study.. Arthritis research & therapy, 2015. PMID 25880754. DOI 10.1186/s13075-015-0590-9. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs healthy control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Control type metadata detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE57376 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Biopsy. Comparison suitability: 0%. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 25333715. - Publication context: Divergent gene activation in peripheral blood and tissues of patients with rheumatoid arthritis, psoriatic arthritis and psoriasis following infliximab therapy.. PloS one, 2014. PMID 25333715. DOI 10.1371/journal.pone.0110657. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs non-lesional tissue. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE57383 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 25333715. - Publication context: Divergent gene activation in peripheral blood and tissues of patients with rheumatoid arthritis, psoriatic arthritis and psoriasis following infliximab therapy.. PloS one, 2014. PMID 25333715. DOI 10.1371/journal.pone.0110657. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: diseased vs healthy control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE57405 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 25333715. - Publication context: Divergent gene activation in peripheral blood and tissues of patients with rheumatoid arthritis, psoriatic arthritis and psoriasis following infliximab therapy.. PloS one, 2014. PMID 25333715. DOI 10.1371/journal.pone.0110657. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs healthy control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Control type metadata detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE63995 Dataset does not meet the current suitability threshold. - Comparison: Treatment vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because it is a treatment/control experiment. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Treated and untreated sample groups detected. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - DOWNGRADE_REASON: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than ten samples limit cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Treatment vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because it is a treatment/control experiment. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison. - WARNING_CODE: TREATED_AND_UNTREATED_SAMPLES_MIXED [info]: Treated and untreated samples are both present. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - TREATED_SAMPLES_NEED_REVIEW [INFO]: Treated samples may need review depending on the comparison.; samples: GSM1562203, GSM1562205, GSM1562207, GSM1562209 - TREATED_AND_UNTREATED_SAMPLES_MIXED [INFO]: Treated and untreated samples are both present.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE65010 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 26314565. - Publication context: Phenotypic, Functional, and Gene Expression Profiling of Peripheral CD45RA+ and CD45RO+ CD4+CD25+CD127(low) Treg Cells in Patients With Chronic Rheumatoid Arthritis.. Arthritis & rheumatology (Hoboken, N.J.), 2016. PMID 26314565. DOI 10.1002/art.39408. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs healthy control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Control type metadata detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE71370 Dataset does not meet the current suitability threshold. - Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 1 DOI available: PMID 28118944, PMID 37573587. - Publication context: MicroRNA-155 contributes to enhanced resistance to apoptosis in monocytes from patients with rheumatoid arthritis.. Journal of autoimmunity, 2017. PMID 28118944. DOI 10.1016/j.jaut.2017.01.002. - Publication context: Dissecting the Imbalance of Synovial Macrophages in Rheumatoid Arthritis.. Alternative therapies in health and medicine, 2023. PMID 37573587. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs healthy control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Control type metadata detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE77298 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Tissue. Comparison suitability: 0%. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 21 publications; 21 DOIs available: PMID 26711533, PMID 38484666, PMID 38491124, PMID 38771826, PMID 38814177. - Publication context: Disease-Regulated Gene Therapy with Anti-Inflammatory Interleukin-10 Under the Control of the CXCL10 Promoter for the Treatment of Rheumatoid Arthritis.. Human gene therapy, 2016. PMID 26711533. DOI 10.1089/hum.2015.127. - Publication context: Integrative analysis and validation of necroptosis-related molecular signature for evaluating diagnosis and immune features in Rheumatoid arthritis.. International immunopharmacology, 2024. PMID 38484666. DOI 10.1016/j.intimp.2024.111809. - Publication context: Identification of Hedyotis diffusa Willd-specific mRNA-miRNA-lncRNA network in rheumatoid arthritis based on network pharmacology, bioinformatics analysis, and experimental verification.. Scientific reports, 2024. PMID 38491124. DOI 10.1038/s41598-024-56880-y. - Publication context: 18 additional linked PubMed publications are available. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs healthy control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Control type metadata detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE83147 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 37814309, PMID 39433011. - Publication context: Identification of the potential regulatory interactions in rheumatoid arthritis through a comprehensive analysis of lncRNA-related ceRNA networks.. BMC musculoskeletal disorders, 2023. PMID 37814309. DOI 10.1186/s12891-023-06936-3. - Publication context: Identification of serum exosomal lncRNAs and their potential regulation of characteristic genes of fibroblast-like synoviocytes in rheumatoid arthritis.. International immunopharmacology, 2024. PMID 39433011. DOI 10.1016/j.intimp.2024.113382. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs normal tissue. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than ten samples limit cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE84074 Dataset does not meet the current suitability threshold. - Comparison: Treatment vs control. Specimen: Biopsy. Comparison suitability: 0%. - Downgraded for tissue search because it is a treatment/control experiment. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 31371761. - Publication context: (5R)-5-Hydroxytriptolide (LLDT-8) induces substantial epigenetic mediated immune response network changes in fibroblast-like synoviocytes from rheumatoid arthritis patients.. Scientific reports, 2019. PMID 31371761. DOI 10.1038/s41598-019-47411-1. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - DOWNGRADE_REASON: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded for tissue search because it is a treatment/control experiment. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison. - WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - TREATED_SAMPLES_NEED_REVIEW [INFO]: Treated samples may need review depending on the comparison.; samples: GSM2226784, GSM2226785, GSM2226786, GSM2226787, GSM2226788, GSM2226789, GSM2226790, GSM2226791, GSM2226792, GSM2226793 - SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE93720 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Tissue. Comparison suitability: 0%. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 28228280. - Publication context: Autocrine Loop Involving IL-6 Family Member LIF, LIF Receptor, and STAT4 Drives Sustained Fibroblast Production of Inflammatory Mediators.. Immunity, 2017. PMID 28228280. DOI 10.1016/j.immuni.2017.01.004. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs untreated. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE93776 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 30013029, PMID 42179742. - Publication context: Multi-omics monitoring of drug response in rheumatoid arthritis in pursuit of molecular remission.. Nature communications, 2018. PMID 30013029. DOI 10.1038/s41467-018-05044-4. - Publication context: Shared gene signatures between rheumatoid arthritis and Sjögren's syndrome.. American journal of clinical and experimental immunology, 2026. PMID 42179742. DOI 10.62347/QHVD4331. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs healthy control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Control type metadata detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE97779 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Mixed specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because specimen/source classes are mixed. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 6 publications; 5 DOIs available: PMID 28813657, PMID 34764682, PMID 36005137, PMID 37573587, PMID 39908806. - Publication context: Interferon-γ Represses M2 Gene Expression in Human Macrophages by Disassembling Enhancers Bound by the Transcription Factor MAF.. Immunity, 2017. PMID 28813657. DOI 10.1016/j.immuni.2017.07.017. - Publication context: Identification of Candidate Genes Related to Synovial Macrophages in Rheumatoid Arthritis by Bioinformatics Analysis.. International journal of general medicine, 2021. PMID 34764682. DOI 10.2147/IJGM.S333512. - Publication context: Classifying Integrated Signature Molecules in Macrophages of Rheumatoid Arthritis, Osteoarthritis, and Periodontal Disease: An Omics-Based Study.. Current issues in molecular biology, 2022. PMID 36005137. DOI 10.3390/cimb44080241. - Publication context: 3 additional linked PubMed publications are available. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs healthy control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - COMPARISON_SUITABILITY: Mixed specimen/source dataset downgraded until tissue samples are clearly separated. - DOWNGRADE_REASON: Mixed specimen/source dataset downgraded until tissue samples are clearly separated. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded for tissue search because specimen/source classes are mixed. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE100648 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Lupus erythematosus, Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 29193869. - Publication context: CD4+ and B Lymphocyte Expression Quantitative Traits at Rheumatoid Arthritis Risk Loci in Patients With Untreated Early Arthritis: Implications for Causal Gene Identification.. Arthritis & rheumatology (Hoboken, N.J.), 2018. PMID 29193869. DOI 10.1002/art.40393. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE100786 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Mixed specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because specimen/source classes are mixed. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 3 publications; 3 DOIs available: PMID 31976312, PMID 33325525, PMID 39315289. - Publication context: Metabonomic-Transcriptome Integration Analysis on Osteoarthritis and Rheumatoid Arthritis.. International journal of genomics, 2020. PMID 31976312. DOI 10.1155/2020/5925126. - Publication context: Identification of novel biomarkers and candidate small molecule drugs in rheumatoid arthritis and osteoarthritis based on bioinformatics analysis of high-throughput data.. Bioscience reports, 2020. PMID 33325525. DOI 10.1042/BSR20193823. - Publication context: Comparison of inflammatory molecular mechanisms between osteoarthritis and rheumatoid arthritis via gene microarrays.. Molecular biology research communications, 2024. PMID 39315289. DOI 10.22099/mbrc.2024.49924.1963. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Mixed specimen/source dataset downgraded until tissue samples are clearly separated. - DOWNGRADE_REASON: Mixed specimen/source dataset downgraded until tissue samples are clearly separated. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Mixed specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because specimen/source classes are mixed. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE103578 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 37814309, PMID 39433011. - Publication context: Identification of the potential regulatory interactions in rheumatoid arthritis through a comprehensive analysis of lncRNA-related ceRNA networks.. BMC musculoskeletal disorders, 2023. PMID 37814309. DOI 10.1186/s12891-023-06936-3. - Publication context: Identification of serum exosomal lncRNAs and their potential regulation of characteristic genes of fibroblast-like synoviocytes in rheumatoid arthritis.. International immunopharmacology, 2024. PMID 39433011. DOI 10.1016/j.intimp.2024.113382. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than ten samples limit cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE107105 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 29476097. - Publication context: Functionally distinct disease-associated fibroblast subsets in rheumatoid arthritis.. Nature communications, 2018. PMID 29476097. DOI 10.1038/s41467-018-02892-y. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE109448 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 29476097, PMID 32637608. - Publication context: Functionally distinct disease-associated fibroblast subsets in rheumatoid arthritis.. Nature communications, 2018. PMID 29476097. DOI 10.1038/s41467-018-02892-y. - Publication context: Synoviocyte-targeted therapy synergizes with TNF inhibition in arthritis reversal.. Science advances, 2020. PMID 32637608. DOI 10.1126/sciadv.aba4353. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE112809 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than ten samples limit cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE12051 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 19847310. - Publication context: An eight-gene blood expression profile predicts the response to infliximab in rheumatoid arthritis.. PloS one, 2009. PMID 19847310. DOI 10.1371/journal.pone.0007556. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE122624 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded for tissue search because study design or specimen source is unclear. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE12653 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 18784373. - Publication context: Mechanisms and pathologic significances in increase in serum interleukin-6 (IL-6) and soluble IL-6 receptor after administration of an anti-IL-6 receptor antibody, tocilizumab, in patients with rheumatoid arthritis and Castleman disease.. Blood, 2008. PMID 18784373. DOI 10.1182/blood-2008-05-155846. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE129486 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 32079724. - Publication context: CUX1 and IκBζ (NFKBIZ) mediate the synergistic inflammatory response to TNF and IL-17A in stromal fibroblasts.. Proceedings of the National Academy of Sciences of the United States of America, 2020. PMID 32079724. DOI 10.1073/pnas.1912702117. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE129705 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded for tissue search because study design or specimen source is unclear. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 31647025. - Publication context: Molecular profiling of rheumatoid arthritis patients reveals an association between innate and adaptive cell populations and response to anti-tumor necrosis factor.. Arthritis research & therapy, 2019. PMID 31647025. DOI 10.1186/s13075-019-1999-3. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE132832 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 31748230. - Publication context: Impaired ATM activation in B cells is associated with bone resorption in rheumatoid arthritis.. Science translational medicine, 2019. PMID 31748230. DOI 10.1126/scitranslmed.aaw4626. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than ten samples limit cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE13917 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 20231422. - Publication context: Complement receptor 2/CD21- human naive B cells contain mostly autoreactive unresponsive clones.. Blood, 2010. PMID 20231422. DOI 10.1182/blood-2009-09-243071. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - TREATED_SAMPLES_NEED_REVIEW [INFO]: Treated samples may need review depending on the comparison.; samples: GSM350574, GSM350575, GSM350577, GSM350578, GSM350581, GSM350583, GSM350587, GSM350589, GSM350601, GSM350602 - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE140036 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 32843099. - Publication context: Lower peripheral helper T cell levels in the synovium are associated with a better response to anti-TNF therapy in rheumatoid arthritis.. Arthritis research & therapy, 2020. PMID 32843099. DOI 10.1186/s13075-020-02287-9. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE146393 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 32765511. - Publication context: Nicotine Changes the microRNA Profile to Regulate the FOXO Memory Program of CD8(+) T Cells in Rheumatoid Arthritis.. Frontiers in immunology, 2020. PMID 32765511. DOI 10.3389/fimmu.2020.01474. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - COMPARISON_SUITABILITY: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking. - DOWNGRADE_REASON: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE15258 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 19699293. - Publication context: Convergent Random Forest predictor: methodology for predicting drug response from genome-scale data applied to anti-TNF response.. Genomics, 2009. PMID 19699293. DOI 10.1016/j.ygeno.2009.08.008. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - TREATED_SAMPLES_NEED_REVIEW [INFO]: Treated samples may need review depending on the comparison.; samples: GSM381194, GSM381195, GSM381196, GSM381197, GSM381198, GSM381199, GSM381200, GSM381201, GSM381202, GSM381203, GSM381204, GSM381205, GSM381206, GSM381207, GSM381208, GSM381209, GSM381210, GSM381211, GSM381212, GSM381213, GSM381214, GSM381215, GSM381216, GSM381217, GSM381218, GSM381219, GSM381220, GSM381221, GSM381222, GSM381223, GSM381224, GSM381225, GSM381226, GSM381227, GSM381228, GSM381229, GSM381230, GSM381231, GSM381232, GSM381233, GSM381234, GSM381235, GSM381236, GSM381237, GSM381238, GSM381239, GSM381240, GSM381241, GSM381242, GSM381243, GSM381244, GSM381245, GSM381246, GSM381247, GSM381248, GSM381249, GSM381250, GSM381251, GSM381252, GSM381253, GSM381254, GSM381255, GSM381256, GSM381257, GSM381258, GSM381259, GSM381260, GSM381261, GSM381262, GSM381263, GSM381264, GSM381265, GSM381266, GSM381267, GSM381268, GSM381269, GSM381270, GSM381271, GSM381272, GSM381273, GSM381274, GSM381275, GSM381276, GSM381277, GSM381278, GSM381279 - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE153015 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 4 publications; 4 DOIs available: PMID 33329580, PMID 36861127, PMID 36940554, PMID 40833035. - Publication context: Paired Rheumatoid Arthritis Synovial Biopsies From Small and Large Joints Show Similar Global Transcriptomic Patterns With Enrichment of Private Specificity TCRB and TCR Signaling Pathways.. Frontiers in immunology, 2020. PMID 33329580. DOI 10.3389/fimmu.2020.593083. - Publication context: Identification of key candidate genes and pathways in rheumatoid arthritis and osteoarthritis by integrated bioinformatical analysis.. Frontiers in genetics, 2023. PMID 36861127. DOI 10.3389/fgene.2023.1083615. - Publication context: Identification and preliminary validation of synovial tissue-specific genes and their-mediated biological mechanisms in rheumatoid arthritis.. International immunopharmacology, 2023. PMID 36940554. DOI 10.1016/j.intimp.2023.109997. - Publication context: 1 additional linked PubMed publications are available. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE15316 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 19842941, PMID 36374432. - Publication context: Identification of candidate genes for rituximab response in rheumatoid arthritis patients by microarray expression profiling in blood cells.. Pharmacogenomics, 2009. PMID 19842941. DOI 10.2217/pgs.09.99. - Publication context: Predictors of response of rituximab in rheumatoid arthritis by weighted gene co-expression network analysis.. Clinical rheumatology, 2023. PMID 36374432. DOI 10.1007/s10067-022-06438-y. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE15602 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Biopsy. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 19389237. - Publication context: Gene expression profiling in the synovium identifies a predictive signature of absence of response to adalimumab therapy in rheumatoid arthritis.. Arthritis research & therapy, 2009. PMID 19389237. DOI 10.1186/ar2678. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biopsy. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - TREATED_SAMPLES_NEED_REVIEW [INFO]: Treated samples may need review depending on the comparison.; samples: GSM390153, GSM390154, GSM390155, GSM390156, GSM390157, GSM390158, GSM390159, GSM390160, GSM390170, GSM390171, GSM390173 - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE15615 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Cultured cells. Comparison suitability: 0%. - Downgraded for tissue search because it is a model-system experiment. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 19389237. - Publication context: Gene expression profiling in the synovium identifies a predictive signature of absence of response to adalimumab therapy in rheumatoid arthritis.. Arthritis research & therapy, 2009. PMID 19389237. DOI 10.1186/ar2678. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Organoid or cell-line experiment downgraded for patient tissue search intent. - DOWNGRADE_REASON: Organoid or cell-line experiment downgraded for patient tissue search intent. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than ten samples limit cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Cultured cells. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because it is a model-system experiment. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: CULTURED_CELL_MODEL_NEEDS_REVIEW [warning]: Cultured primary, endothelial, macrophage, or stem-cell samples were detected; interpret these as an experimental model rather than a patient biofluid or tissue cohort. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - CULTURED_CELL_MODEL_NEEDS_REVIEW [WARNING]: Cultured primary, endothelial, macrophage, or stem-cell samples were detected; interpret these as an experimental model rather than a patient biofluid or tissue cohort.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE172188 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 34526997. - Publication context: Common Transcriptomic Effects of Abatacept and Other DMARDs on Rheumatoid Arthritis Synovial Tissue.. Frontiers in immunology, 2021. PMID 34526997. DOI 10.3389/fimmu.2021.724895. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE176440 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 35659346. - Publication context: Semaphorin 3G exacerbates joint inflammation through the accumulation and proliferation of macrophages in the synovium.. Arthritis research & therapy, 2022. PMID 35659346. DOI 10.1186/s13075-022-02817-7. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE18097 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Control type metadata detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - COMPARISON_SUITABILITY: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking. - DOWNGRADE_REASON: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than six samples are too small for top-ranked cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than six samples are too small for top-ranked cohort confidence. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: SAMPLE_COUNT_BELOW_THRESHOLD [warning]: Total sample count is below the minimum needed for two comparison groups. - WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - SAMPLE_COUNT_BELOW_THRESHOLD [WARNING]: Total sample count is below the minimum needed for two comparison groups.; samples: - SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE199152 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Biopsy. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Fibrosis, Idiopathic pulmonary fibrosis, Lung fibrosis, Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 38571583, PMID 40418457. - Publication context: Identification and validation of mutual hub genes in idiopathic pulmonary fibrosis and rheumatoid arthritis-associated usual interstitial pneumonia.. Heliyon, 2024. PMID 38571583. DOI 10.1016/j.heliyon.2024.e28088. - Publication context: Triptolide Ameliorates Collagen-Induced Arthritis and Bleomycin-Induced Pulmonary Fibrosis in Rats by Suppressing IGF1-Mediated Epithelial Mesenchymal Transition.. Chinese journal of integrative medicine, 2025. PMID 40418457. DOI 10.1007/s11655-025-4224-z. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biopsy. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE21385 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data availability is missing or unclear. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 20462438. - Publication context: Cell culture and passaging alters gene expression pattern and proliferation rate in rheumatoid arthritis synovial fibroblasts.. Arthritis research & therapy, 2010. PMID 20462438. DOI 10.1186/ar3010. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level data availability is explicit, even though no downloadable data is available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - MISSING_METADATA: Missing or unclear metadata. Processed data availability is missing or unclear. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: PROCESSED_COUNTS_NOT_FOUND [warning]: Processed count data was not found in the dataset index. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - PROCESSED_COUNTS_NOT_FOUND [WARNING]: Processed count data was not found in the dataset index.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE21537 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Biopsy. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 20593016. - Publication context: The gene expression profile in the synovium as a predictor of the clinical response to infliximab treatment in rheumatoid arthritis.. PloS one, 2010. PMID 20593016. DOI 10.1371/journal.pone.0011310. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biopsy. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE224842 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE225731 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 37507201. - Publication context: Disease activity drives transcriptomic heterogeneity in early untreated rheumatoid synovitis.. Annals of the rheumatic diseases, 2023. PMID 37507201. DOI 10.1136/ard-2023-224068. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE261149 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than ten samples limit cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE263015 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis, Tuberculosis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 41611143. - Publication context: Stage-specific miRNA signatures in osteoarthritis identify miR-4505 and miR-331-3p as key modulators of disease pathogenesis via ERBB2 suppression.. International journal of biological macromolecules, 2026. PMID 41611143. DOI 10.1016/j.ijbiomac.2026.150525. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - COMPARISON_SUITABILITY: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking. - DOWNGRADE_REASON: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE27390 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 21679443, PMID 25118911. - Publication context: Abnormal networks of immune response-related molecules in bone marrow cells from patients with rheumatoid arthritis as revealed by DNA microarray analysis.. Arthritis research & therapy, 2011. PMID 21679443. DOI 10.1186/ar3364. - Publication context: Differential co-expression analysis of rheumatoid arthritis with microarray data.. Molecular medicine reports, 2014. PMID 25118911. DOI 10.3892/mmr.2014.2491. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE279719 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded for tissue search because study design or specimen source is unclear. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE30023 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Infectious disease or host response, Rheumatoid arthritis. - Processed data is available for downstream review. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE311923 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than ten samples limit cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE31685 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Cultured cells. Comparison suitability: 0%. - Downgraded for tissue search because it is a model-system experiment. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Organoid or cell-line experiment downgraded for patient tissue search intent. - DOWNGRADE_REASON: Organoid or cell-line experiment downgraded for patient tissue search intent. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than ten samples limit cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Cultured cells. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because it is a model-system experiment. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: CULTURED_CELL_MODEL_NEEDS_REVIEW [warning]: Cultured primary, endothelial, macrophage, or stem-cell samples were detected; interpret these as an experimental model rather than a patient biofluid or tissue cohort. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - TREATED_SAMPLES_NEED_REVIEW [INFO]: Treated samples may need review depending on the comparison.; samples: GSM786584, GSM786585, GSM786586, GSM786587, GSM786588, GSM786589 - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - CULTURED_CELL_MODEL_NEEDS_REVIEW [WARNING]: Cultured primary, endothelial, macrophage, or stem-cell samples were detected; interpret these as an experimental model rather than a patient biofluid or tissue cohort.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE35455 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE36700 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Lupus erythematosus, Rheumatoid arthritis, Systemic lupus erythematosus. - Processed data is available for downstream review. - External evidence: PubMed links 9 publications; 9 DOIs available: PMID 17469140, PMID 25927832, PMID 28818099, PMID 30260019, PMID 30483789. - Publication context: Identification of distinct gene expression profiles in the synovium of patients with systemic lupus erythematosus.. Arthritis and rheumatism, 2007. PMID 17469140. DOI 10.1002/art.22578. - Publication context: Heterogeneity of synovial molecular patterns in patients with arthritis.. PloS one, 2015. PMID 25927832. DOI 10.1371/journal.pone.0122104. - Publication context: Biosemantics guided gene expression profiling of Sjögren's syndrome: a comparative analysis with systemic lupus erythematosus and rheumatoid arthritis.. Arthritis research & therapy, 2017. PMID 28818099. DOI 10.1186/s13075-017-1400-3. - Publication context: 6 additional linked PubMed publications are available. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE36757 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than six samples are too small for top-ranked cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than six samples are too small for top-ranked cohort confidence. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison. - WARNING_CODE: SAMPLE_COUNT_BELOW_THRESHOLD [warning]: Total sample count is below the minimum needed for two comparison groups. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - TREATED_SAMPLES_NEED_REVIEW [INFO]: Treated samples may need review depending on the comparison.; samples: GSM900415 - SAMPLE_COUNT_BELOW_THRESHOLD [WARNING]: Total sample count is below the minimum needed for two comparison groups.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE37107 Dataset does not meet the current suitability threshold. - Comparison: Treatment vs control. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded for tissue search because it is a treatment/control experiment. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 22540992, PMID 36374432. - Publication context: The interferon type I signature towards prediction of non-response to rituximab in rheumatoid arthritis patients.. Arthritis research & therapy, 2012. PMID 22540992. DOI 10.1186/ar3819. - Publication context: Predictors of response of rituximab in rheumatoid arthritis by weighted gene co-expression network analysis.. Clinical rheumatology, 2023. PMID 36374432. DOI 10.1007/s10067-022-06438-y. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - DOWNGRADE_REASON: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded for tissue search because it is a treatment/control experiment. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison. - WARNING_CODE: TREATED_AND_UNTREATED_SAMPLES_MIXED [info]: Treated and untreated samples are both present. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - TREATED_SAMPLES_NEED_REVIEW [INFO]: Treated samples may need review depending on the comparison.; samples: GSM910736, GSM910737, GSM910738, GSM910739, GSM910740, GSM910741, GSM910742, GSM910743, GSM910744, GSM910745, GSM910746, GSM910747, GSM910748, GSM910749 - TREATED_AND_UNTREATED_SAMPLES_MIXED [INFO]: Treated and untreated samples are both present.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE38064 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 30114200. - Publication context: Co-expression of CD21L and IL17A defines a subset of rheumatoid synovia, characterised by large lymphoid aggregates and high inflammation.. PloS one, 2018. PMID 30114200. DOI 10.1371/journal.pone.0202135. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE39340 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 3 publications; 2 DOIs available: PMID 33040798, PMID 33052895, PMID 36173499. - Publication context: PDGFRB as a potential therapeutic target of ankylosing spondylitis: validation following bioinformatics analysis.. Cellular and molecular biology (Noisy-le-Grand, France), 2020. PMID 33040798. - Publication context: A Mechanism Underlying Sex-Associated Differences in Ankylosing Spondylitis: Troponin C2, Fast Skeletal Type (TNNC2) and Calcium Signaling Pathway.. Medical science monitor : international medical journal of experimental and clinical research, 2020. PMID 33052895. DOI 10.12659/MSM.925179. - Publication context: Identification of key genes and pathways associated with sex differences in rheumatoid arthritis based on bioinformatics analysis.. Clinical rheumatology, 2023. PMID 36173499. DOI 10.1007/s10067-022-06387-6. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE42296 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Crohn's disease, Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 23809696, PMID 32104045. - Publication context: Peripheral blood derived gene panels predict response to infliximab in rheumatoid arthritis and Crohn's disease.. Genome medicine, 2013. PMID 23809696. DOI 10.1186/gm463. - Publication context: Integrated Gene Expression Profiling Analysis Reveals Probable Molecular Mechanism and Candidate Biomarker in Anti-TNFα Non-Response IBD Patients.. Journal of inflammation research, 2020. PMID 32104045. DOI 10.2147/JIR.S236262. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE42842 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE4588 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Lupus erythematosus, Rheumatoid arthritis, Systemic lupus erythematosus. - Processed data is available for downstream review. - External evidence: PubMed links 4 publications; 4 DOIs available: PMID 33468161, PMID 34149710, PMID 34160465, PMID 35757721. - Publication context: Identification of key biomarkers and immune infiltration in systemic lupus erythematosus by integrated bioinformatics analysis.. Journal of translational medicine, 2021. PMID 33468161. DOI 10.1186/s12967-020-02698-x. - Publication context: CD3(+)CD4(+)gp130(+) T Cells Are Associated With Worse Disease Activity in Systemic Lupus Erythematosus Patients.. Frontiers in immunology, 2021. PMID 34149710. DOI 10.3389/fimmu.2021.675250. - Publication context: Identification of hub genes, pathways, and related transcription factors in systemic lupus erythematosus: A preliminary bioinformatics analysis.. Medicine, 2021. PMID 34160465. DOI 10.1097/MD.0000000000026499. - Publication context: 1 additional linked PubMed publications are available. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE47726 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 31312201, PMID 32843099. - Publication context: A Combined Transcriptomic and Genomic Analysis Identifies a Gene Signature Associated With the Response to Anti-TNF Therapy in Rheumatoid Arthritis.. Frontiers in immunology, 2019. PMID 31312201. DOI 10.3389/fimmu.2019.01459. - Publication context: Lower peripheral helper T cell levels in the synovium are associated with a better response to anti-TNF therapy in rheumatoid arthritis.. Arthritis research & therapy, 2020. PMID 32843099. DOI 10.1186/s13075-020-02287-9. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE48780 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Mixed specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because specimen/source classes are mixed. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 3 publications; 3 DOIs available: PMID 24935926, PMID 26404854, PMID 39080453. - Publication context: PILRα negatively regulates mouse inflammatory arthritis.. Journal of immunology (Baltimore, Md. : 1950), 2014. PMID 24935926. DOI 10.4049/jimmunol.1400045. - Publication context: Analysis of differences in the molecular mechanism of rheumatoid arthritis and osteoarthritis based on integration of gene expression profiles.. Immunology letters, 2015. PMID 26404854. DOI 10.1016/j.imlet.2015.09.011. - Publication context: Identification of the ferroptosis-related gene signature and the associated regulation axis in lung cancer and rheumatoid arthritis.. Genes and immunity, 2024. PMID 39080453. DOI 10.1038/s41435-024-00287-2. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Mixed specimen/source dataset downgraded until tissue samples are clearly separated. - DOWNGRADE_REASON: Mixed specimen/source dataset downgraded until tissue samples are clearly separated. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Mixed specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because specimen/source classes are mixed. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE55584 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 13 publications; 12 DOIs available: PMID 24690414, PMID 29344651, PMID 30091955, PMID 30483789, PMID 31309562. - Publication context: Identification of rheumatoid arthritis and osteoarthritis patients by transcriptome-based rule set generation.. Arthritis research & therapy, 2014. PMID 24690414. DOI 10.1186/ar4526. - Publication context: Identification of genes and pathways in the synovia of women with osteoarthritis by bioinformatics analysis.. Molecular medicine reports, 2018. PMID 29344651. DOI 10.3892/mmr.2018.8429. - Publication context: Identification of Key Genes and Pathways in Rheumatoid Arthritis Gene Expression Profile by Bioinformatics.. Acta reumatologica portuguesa, 2018. PMID 30091955. - Publication context: 10 additional linked PubMed publications are available. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE56409 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 3 publications; 3 DOIs available: PMID 25807374, PMID 34195267, PMID 37741987. - Publication context: Stromal transcriptional profiles reveal hierarchies of anatomical site, serum response and disease and identify disease specific pathways.. PloS one, 2015. PMID 25807374. DOI 10.1371/journal.pone.0120917. - Publication context: Marker Genes Change of Synovial Fibroblasts in Rheumatoid Arthritis Patients.. BioMed research international, 2021. PMID 34195267. DOI 10.1155/2021/5544264. - Publication context: Synovium is a sensitive tissue for mapping the negative effects of systemic iron overload in osteoarthritis: identification and validation of two potential targets.. Journal of translational medicine, 2023. PMID 37741987. DOI 10.1186/s12967-023-04541-5. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE59526 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 40636547. - Publication context: Identifying Diagnostic Biomarkers for Electroacupuncture Treatment of Rheumatoid Arthritis Using Bioinformatic Analysis and Machine Learning Algorithms.. Journal of pain research, 2025. PMID 40636547. DOI 10.2147/JPR.S517733. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - TREATED_SAMPLES_NEED_REVIEW [INFO]: Treated samples may need review depending on the comparison.; samples: GSM1438872, GSM1438873, GSM1438874, GSM1438875, GSM1438876, GSM1438877, GSM1438878, GSM1438879, GSM1438880, GSM1438881 - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE60649 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Other non-gastrointestinal cancer, Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 25199827. - Publication context: Myeloid malignancies with chromosome 5q deletions acquire a dependency on an intrachromosomal NF-κB gene network.. Cell reports, 2014. PMID 25199827. DOI 10.1016/j.celrep.2014.07.062. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than ten samples limit cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE66084 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 26171167. - Publication context: Characteristic expression of MSX1, MSX2, TBX2 and ENTPD1 in dental pulp cells.. Biomedical reports, 2015. PMID 26171167. DOI 10.3892/br.2015.456. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE72258 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 26316022. - Publication context: C5orf30 is a negative regulator of tissue damage in rheumatoid arthritis.. Proceedings of the National Academy of Sciences of the United States of America, 2015. PMID 26316022. DOI 10.1073/pnas.1501947112. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE73764 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 26792343. - Publication context: Higher expression of TNFα-induced genes in the synovium of patients with early rheumatoid arthritis correlates with disease activity, and predicts absence of response to first line therapy.. Arthritis research & therapy, 2016. PMID 26792343. DOI 10.1186/s13075-016-0919-z. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than six samples are too small for top-ranked cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than six samples are too small for top-ranked cohort confidence. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison. - WARNING_CODE: SMALL_COHORT_NEEDS_REVIEW [warning]: Dataset has fewer than six samples and should not be treated as a high-confidence cohort without manual review. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - TREATED_SAMPLES_NEED_REVIEW [INFO]: Treated samples may need review depending on the comparison.; samples: GSM1902359, GSM1902361 - SMALL_COHORT_NEEDS_REVIEW [WARNING]: Dataset has fewer than six samples and should not be treated as a high-confidence cohort without manual review.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE74143 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 27140173. - Publication context: Integrative genomic deconvolution of rheumatoid arthritis GWAS loci into gene and cell type associations.. Genome biology, 2016. PMID 27140173. DOI 10.1186/s13059-016-0948-6. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE7524 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than ten samples limit cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE78068 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 27435242, PMID 35046954. - Publication context: Identification of baseline gene expression signatures predicting therapeutic responses to three biologic agents in rheumatoid arthritis: a retrospective observational study.. Arthritis research & therapy, 2016. PMID 27435242. DOI 10.1186/s13075-016-1052-8. - Publication context: Derlin-1, as a Potential Early Predictive Biomarker for Nonresponse to Infliximab Treatment in Rheumatoid Arthritis, Is Related to Autophagy.. Frontiers in immunology, 2021. PMID 35046954. DOI 10.3389/fimmu.2021.795912. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE80785 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE91026 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 28775366. - Publication context: MicroRNA-143 and -145 modulate the phenotype of synovial fibroblasts in rheumatoid arthritis.. Experimental & molecular medicine, 2017. PMID 28775366. DOI 10.1038/emm.2017.108. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - COMPARISON_SUITABILITY: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking. - DOWNGRADE_REASON: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than ten samples limit cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison. - WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - TREATED_SAMPLES_NEED_REVIEW [INFO]: Treated samples may need review depending on the comparison.; samples: GSM2419891, GSM2419892, GSM2419893, GSM2419894, GSM2419895, GSM2419896, GSM2419897, GSM2419898 - SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE9329 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 18187038. - Publication context: Involvement of thioredoxin reductase 1 in the regulation of redox balance and viability of rheumatoid synovial cells.. Biochemical and biophysical research communications, 2008. PMID 18187038. DOI 10.1016/j.bbrc.2007.12.178. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than six samples are too small for top-ranked cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than six samples are too small for top-ranked cohort confidence. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: SAMPLE_COUNT_BELOW_THRESHOLD [warning]: Total sample count is below the minimum needed for two comparison groups. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - SAMPLE_COUNT_BELOW_THRESHOLD [WARNING]: Total sample count is below the minimum needed for two comparison groups.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE93698 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Biopsy. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Fibrosis, Lupus erythematosus, Rheumatoid arthritis, Systemic lupus erythematosus, Systemic sclerosis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 30608617. - Publication context: Overexpression of ubiquitin-specific peptidase 15 in systemic sclerosis fibroblasts increases response to transforming growth factor β.. Rheumatology (Oxford, England), 2019. PMID 30608617. DOI 10.1093/rheumatology/key401. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biopsy. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE94897 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded for tissue search because study design or specimen source is unclear. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: recount3 reports trusted processed count availability. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 28664171. - Publication context: Immunoglobulin characteristics and RNAseq data of FcRL4+ B cells sorted from synovial fluid and tissue of patients with rheumatoid arthritis.. Data in brief, 2017. PMID 28664171. DOI 10.1016/j.dib.2017.06.009. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than ten samples limit cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biofluid. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE38351 Dataset does not meet the current suitability threshold. - Comparison: Treatment vs control. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded for tissue search because it is a treatment/control experiment. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis, Systemic lupus erythematosus. - Processed data is available for downstream review. - External evidence: Expression Atlas curated experiment link is available. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 19265543, PMID 22610275. - Publication context: SiPaGene: A new repository for instant online retrieval, sharing and meta-analyses of GeneChip expression data.. BMC genomics, 2009. PMID 19265543. DOI 10.1186/1471-2164-10-98. - Publication context: The multifaceted balance of TNF-α and type I/II interferon responses in SLE and RA: how monocytes manage the impact of cytokines.. Journal of molecular medicine (Berlin, Germany), 2012. PMID 22610275. DOI 10.1007/s00109-012-0907-y. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: systemic lupus erythematosus vs healthy control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Control type metadata detected. - COMPARISON_SUITABILITY: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - DOWNGRADE_REASON: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Pooled or technical replicate samples reduce suitability. - DOWNGRADE_REASON: Pooled or technical replicate samples reduce suitability. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: Pooled samples or technical replicates need review before trusting group counts. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded for tissue search because it is a treatment/control experiment. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: TECHNICAL_REPLICATES_DETECTED [warning]: Technical replicate samples were detected. - WARNING_CODE: TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - TECHNICAL_REPLICATES_DETECTED [WARNING]: Technical replicate samples were detected.; samples: GSM940482, GSM940483 - TREATED_SAMPLES_NEED_REVIEW [INFO]: Treated samples may need review depending on the comparison.; samples: GSM940488, GSM940489, GSM940490, GSM940491, GSM940492, GSM940493, GSM940494, GSM940495, GSM940496, GSM940497, GSM940498, GSM940499, GSM940500, GSM940501, GSM940502, GSM940503, GSM940504 - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE118958 Dataset does not meet the current suitability threshold. - Comparison: Treatment vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because it is a treatment/control experiment. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 31258900. - Publication context: Expression profiling of genes in rheumatoid fibroblast-like synoviocytes regulated by tumor necrosis factor-like ligand 1A using cDNA microarray analysis.. Biomedical reports, 2019. PMID 31258900. DOI 10.3892/br.2019.1216. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - DOWNGRADE_REASON: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Tissue metadata was not normalized. - MISSING_METADATA: Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than ten samples limit cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Treatment vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because it is a treatment/control experiment. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: TISSUE_TYPE_MISSING [warning]: Tissue or cell type could not be normalized. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - TREATED_SAMPLES_NEED_REVIEW [INFO]: Treated samples may need review depending on the comparison.; samples: GSM3354765, GSM3354766, GSM3354767, GSM3354768, GSM3354769, GSM3354770, GSM3354771, GSM3354772 - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - TISSUE_TYPE_MISSING [WARNING]: Tissue or cell type could not be normalized.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE145204 Dataset does not meet the current suitability threshold. - Comparison: Treatment vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because it is a treatment/control experiment. - Downgraded for tissue search because study design or specimen source is unclear. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - COMPARISON_SUITABILITY: Treated and untreated sample groups detected. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - DOWNGRADE_REASON: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Tissue metadata was not normalized. - MISSING_METADATA: Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Treatment vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because it is a treatment/control experiment. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - WARNING_CODE: TISSUE_TYPE_MISSING [warning]: Tissue or cell type could not be normalized. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - TISSUE_TYPE_MISSING [WARNING]: Tissue or cell type could not be normalized.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE200030 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 35941675. - Publication context: Regulation of type I interferon signature by VGLL3 in the fibroblast-like synoviocytes of rheumatoid arthritis patients via targeting the Hippo pathway.. Arthritis research & therapy, 2022. PMID 35941675. DOI 10.1186/s13075-022-02880-0. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: overexpression vs genetic control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Tissue metadata was not normalized. - MISSING_METADATA: Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than six samples are too small for top-ranked cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than six samples are too small for top-ranked cohort confidence. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - WARNING_CODE: SAMPLE_COUNT_BELOW_THRESHOLD [warning]: Total sample count is below the minimum needed for two comparison groups. - WARNING_CODE: TISSUE_TYPE_MISSING [warning]: Tissue or cell type could not be normalized. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - SAMPLE_COUNT_BELOW_THRESHOLD [WARNING]: Total sample count is below the minimum needed for two comparison groups.; samples: - TISSUE_TYPE_MISSING [WARNING]: Tissue or cell type could not be normalized.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE22956 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 21717420. - Publication context: NF-AT5 is a critical regulator of inflammatory arthritis.. Arthritis and rheumatism, 2011. PMID 21717420. DOI 10.1002/art.30229. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs control. - COMPARISON_SUITABILITY: Excluded sample type flags reduce suitability. - DOWNGRADE_REASON: Excluded sample type flags reduce suitability. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Excluded model-system sample markers reduce suitability. - DOWNGRADE_REASON: Excluded model-system sample markers reduce suitability. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Tissue metadata was not normalized. - MISSING_METADATA: Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: MIXED_SAMPLE_TYPES [warning]: Multiple sample type labels or exclusion flags were detected. - WARNING_CODE: CELL_LINES_INCLUDED [warning]: Cell line samples appear to be included. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: TISSUE_TYPE_MISSING [warning]: Tissue or cell type could not be normalized. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - MIXED_SAMPLE_TYPES [WARNING]: Multiple sample type labels or exclusion flags were detected.; samples: - CELL_LINES_INCLUDED [WARNING]: Cell line samples appear to be included.; samples: GSM566728, GSM566729, GSM566730, GSM566731, GSM566732, GSM566733, GSM566734, GSM566735, GSM566736, GSM566737, GSM566738, GSM566739 - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - TISSUE_TYPE_MISSING [WARNING]: Tissue or cell type could not be normalized.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE266310 Dataset does not meet the current suitability threshold. - Comparison: Treatment vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because it is a treatment/control experiment. - Downgraded for tissue search because study design or specimen source is unclear. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 39394168. - Publication context: Methotrexate promotes the release of granulocyte-macrophage colony-stimulating factor from rheumatoid arthritis fibroblast-like synoviocytes via autocrine interleukin-1 signaling.. Arthritis research & therapy, 2024. PMID 39394168. DOI 10.1186/s13075-024-03406-6. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: MTX-treated vs no named treatment control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - DOWNGRADE_REASON: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Tissue metadata was not normalized. - MISSING_METADATA: Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than ten samples limit cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Treatment vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because it is a treatment/control experiment. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - WARNING_CODE: TISSUE_TYPE_MISSING [warning]: Tissue or cell type could not be normalized. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - TISSUE_TYPE_MISSING [WARNING]: Tissue or cell type could not be normalized.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE2779 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 5 publications; 5 DOIs available: PMID 16076868, PMID 23301083, PMID 31411003, PMID 32772642, PMID 36166051. - Publication context: Evidence for reduced B-cell progenitors in early (low-risk) myelodysplastic syndrome.. Blood, 2005. PMID 16076868. DOI 10.1182/blood-2005-04-1543. - Publication context: Visualising the cross-level relationships between pathological and physiological processes and gene expression: analyses of haematological diseases.. PloS one, 2013. PMID 23301083. DOI 10.1371/journal.pone.0053544. - Publication context: Expression significance and potential mechanism of hypoxia-inducible factor 1 alpha in patients with myelodysplastic syndromes.. Cancer medicine, 2019. PMID 31411003. DOI 10.1002/cam4.2447. - Publication context: 2 additional linked PubMed publications are available. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs normal tissue. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - DOWNGRADE_REASON: Disease/control design without a tumor/normal comparison is outside tumor/normal triage. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Tissue metadata was not normalized. - MISSING_METADATA: Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - DOWNGRADE_REASON: Publication context: Evidence for reduced B-cell progenitors in early (low-risk) myelodysplastic syndrome.. Blood, 2005. PMID 16076868. DOI 10.1182/blood-2005-04-1543. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: TISSUE_TYPE_MISSING [warning]: Tissue or cell type could not be normalized. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - TISSUE_TYPE_MISSING [WARNING]: Tissue or cell type could not be normalized.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE300831 Dataset does not meet the current suitability threshold. - Comparison: Treatment vs control. Specimen: Cell line. Comparison suitability: 0%. - Downgraded for tissue search because it is a model-system experiment. - Downgraded for tissue search because it is a treatment/control experiment. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - COMPARISON_SUITABILITY: Treated and untreated sample groups detected. - COMPARISON_SUITABILITY: Excluded sample type flags reduce suitability. - DOWNGRADE_REASON: Excluded sample type flags reduce suitability. - COMPARISON_SUITABILITY: Control type metadata detected. - COMPARISON_SUITABILITY: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - DOWNGRADE_REASON: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - COMPARISON_SUITABILITY: Organoid or cell-line experiment downgraded for patient tissue search intent. - DOWNGRADE_REASON: Organoid or cell-line experiment downgraded for patient tissue search intent. - COMPARISON_SUITABILITY: Excluded model-system sample markers reduce suitability. - DOWNGRADE_REASON: Excluded model-system sample markers reduce suitability. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Tissue metadata was not normalized. - MISSING_METADATA: Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded for tissue search because it is a model-system experiment. - DOWNGRADE_REASON: Downgraded for tissue search because it is a treatment/control experiment. - WARNING_CODE: MIXED_SAMPLE_TYPES [warning]: Multiple sample type labels or exclusion flags were detected. - WARNING_CODE: CELL_LINES_INCLUDED [warning]: Cell line samples appear to be included. - MIXED_SAMPLE_TYPES [WARNING]: Multiple sample type labels or exclusion flags were detected.; samples: - CELL_LINES_INCLUDED [WARNING]: Cell line samples appear to be included.; samples: GSM9069336, GSM9069337, GSM9069338, GSM9069339, GSM9069340, GSM9069341, GSM9069342, GSM9069343, GSM9069344, GSM9069345, GSM9069346, GSM9069347 ### GSE45665 Dataset does not meet the current suitability threshold. - Comparison: Treatment vs control. Specimen: Tissue. Comparison suitability: 0%. - Downgraded for tissue search because it is a treatment/control experiment. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 23912906. - Publication context: Decoy receptor 3 regulates the expression of various genes in rheumatoid arthritis synovial fibroblasts.. International journal of molecular medicine, 2013. PMID 23912906. DOI 10.3892/ijmm.2013.1461. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - DOWNGRADE_REASON: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Tissue metadata was not normalized. - MISSING_METADATA: Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than ten samples limit cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded for tissue search because it is a treatment/control experiment. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - TREATED_SAMPLES_NEED_REVIEW [INFO]: Treated samples may need review depending on the comparison.; samples: GSM1111504, GSM1111505, GSM1111506, GSM1111507, GSM1111508, GSM1111509, GSM1111510, GSM1111511 - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE94519 Dataset does not meet the current suitability threshold. - Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 0%. - Downgraded for tissue search because it is a biofluid cohort. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 3 publications; 3 DOIs available: PMID 36405992, PMID 36940554, PMID 40279008. - Publication context: ST3GAL3 Promotes the Inflammatory Response of Fibroblast-Like Synoviocytes in Rheumatoid Arthritis by Activating the TLR9/MyD88 Pathway.. Mediators of inflammation, 2022. PMID 36405992. DOI 10.1155/2022/4258742. - Publication context: Identification and preliminary validation of synovial tissue-specific genes and their-mediated biological mechanisms in rheumatoid arthritis.. International immunopharmacology, 2023. PMID 36940554. DOI 10.1016/j.intimp.2023.109997. - Publication context: Dual roles of LncRNA RNA143598: a biomarker for rheumatoid arthritis and its implications in cancer.. Clinical rheumatology, 2025. PMID 40279008. DOI 10.1007/s10067-025-07448-2. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: rheumatoid arthritis vs healthy control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Control type metadata detected. - COMPARISON_SUITABILITY: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - DOWNGRADE_REASON: Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Tissue metadata was not normalized. - MISSING_METADATA: Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than ten samples limit cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded for tissue search because it is a biofluid cohort. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: ### GSE243821 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Tissue metadata was not normalized. - MISSING_METADATA: Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than ten samples limit cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: TISSUE_TYPE_MISSING [warning]: Tissue or cell type could not be normalized. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - TISSUE_TYPE_MISSING [WARNING]: Tissue or cell type could not be normalized.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE267979 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Biopsy. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 39837478. - Publication context: Tissue degrading and remodelling molecules in giant cell arteritis.. Rheumatology (Oxford, England), 2025. PMID 39837478. DOI 10.1093/rheumatology/keae710. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Tissue metadata was not normalized. - MISSING_METADATA: Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Biopsy. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: MIXED_DISEASE_COHORT [warning]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - MIXED_DISEASE_COHORT [WARNING]: Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE33377 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 22457743, PMID 40908203. - Publication context: Validation study of existing gene expression signatures for anti-TNF treatment in patients with rheumatoid arthritis.. PloS one, 2012. PMID 22457743. DOI 10.1371/journal.pone.0033199. - Publication context: Identification of a novel transcriptome signature for predicting the response to anti-TNF-α treatment in patients with rheumatoid arthritis.. Annals of the rheumatic diseases, 2026. PMID 40908203. DOI 10.1016/j.ard.2025.08.003. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Tissue metadata was not normalized. - MISSING_METADATA: Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: TISSUE_TYPE_MISSING [warning]: Tissue or cell type could not be normalized. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - TISSUE_TYPE_MISSING [WARNING]: Tissue or cell type could not be normalized.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE37427 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Lupus erythematosus, Rheumatoid arthritis, Systemic lupus erythematosus. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 22660635. - Publication context: The microRNA miR-23b suppresses IL-17-associated autoimmune inflammation by targeting TAB2, TAB3 and IKK-α.. Nature medicine, 2012. PMID 22660635. DOI 10.1038/nm.2815. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - COMPARISON_SUITABILITY: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - DOWNGRADE_REASON: Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking. - COMPARISON_SUITABILITY: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking. - DOWNGRADE_REASON: Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Tissue metadata was not normalized. - MISSING_METADATA: Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because fewer than six samples are too small for top-ranked cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than six samples are too small for top-ranked cohort confidence. - OVERALL: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - DOWNGRADE_REASON: Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: SAMPLE_COUNT_BELOW_THRESHOLD [warning]: Total sample count is below the minimum needed for two comparison groups. - WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: TISSUE_TYPE_MISSING [warning]: Tissue or cell type could not be normalized. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - SAMPLE_COUNT_BELOW_THRESHOLD [WARNING]: Total sample count is below the minimum needed for two comparison groups.; samples: - SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - TISSUE_TYPE_MISSING [WARNING]: Tissue or cell type could not be normalized.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE55468 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Rheumatoid arthritis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 24959711. - Publication context: Novel insights into the regulatory architecture of CD4+ T cells in rheumatoid arthritis.. PloS one, 2014. PMID 24959711. DOI 10.1371/journal.pone.0100690. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Tissue metadata was not normalized. - MISSING_METADATA: Missing or unclear metadata. Tissue clarity - Tissue metadata was not normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: