# 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:** 2026-10-27T11:44:57.478672777Z - **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: Inflammatory bowel disease - **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=Inflammatory bowel disease; 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: Inflammatory bowel disease - **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: Inflammatory bowel disease - **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 | [GSE141174](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE141174) | Genome-wide analysis of colorectal cancer gene expression by using primary tumors, normal colon and lymph nodes | none | Tumor vs unmatched normal | Tissue | suitability 100; metadata 100; overall 100 | 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=GSE141174) | Needs manual review | | 2 | [GSE92472](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE92472) | Expression of long non-coding RNAs in autoimmunity and linkage to enhancer function and autoimmune disease risk genetic variants | 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=GSE92472) | Exploratory only | | 3 | [GSE100833](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100833) | A functional genomics predictive network model identifies regulators of inflammatory bowel disease: Microarray Analysis of Human Blood and Intestinal Biopsy Samples from a Phase 2b, Double-blind, Placebo-controlled Study of Ustekinumab in Crohn's Disease | none | Treatment 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.; 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=GSE100833) | Not suitable | | 4 | [GSE102133](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE102133) | Mucosal gene expression profiling in ileum of patients with Crohn's disease | 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.; 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=GSE102133) | Not suitable | | 5 | [GSE10616](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10616) | Human colon expression in healthy controls, colon-only CD, ileo-colonic CD, and UC | 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=GSE10616) | Not suitable | | 6 | [GSE107499](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE107499) | Expression data from Ulcerative Colitis subjects | 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.; 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=GSE107499) | Not suitable | | 7 | [GSE10791](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10791) | Gene expression profiles in sigmoid colon biopsies from healthy and patients with ulcerative colitis | none | Disease/model vs control | Biopsy | 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=GSE10791) | Not suitable | | 8 | [GSE110186](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110186) | NOD2- and disease-specific gene expression profiles of peripheral blood mononuclear cells from Crohn’s disease patients | none | Treatment 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=GSE110186) | Not suitable | | 9 | [GSE111889](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE111889) | Longitudinal Multi’omics of the Human Microbiome in Inflammatory Bowel Disease | none | Disease/model vs control | Biopsy | 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=GSE111889) | Not suitable | | 10 | [GSE112057](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE112057) | Whole Blood Transcriptome Profiling in Juvenile Idiopathic Arthritis and Inflammatory Bowel Disease | none | Disease/model vs control | Biofluid | suitability 0; metadata 100; overall 34 | none | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE112057) | Not suitable | | 11 | [GSE11223](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11223) | Colon biopsies from UC patients and healthy controls | none | Treatment vs control | Biofluid | suitability 0; metadata 100; overall 34 | MIXED_SAMPLE_TYPES [warning]: Multiple sample type labels or exclusion flags 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.; 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=GSE11223) | Not suitable | | 12 | [GSE112366](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE112366) | Intestinal epithelial microvilli are abnormal in Crohn's disease | none | Treatment vs control | Biopsy | 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=GSE112366) | Not suitable | | 13 | [GSE1141](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1141) | Inflammatory bowel disease (HG-U133A) | 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.; 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=GSE1141) | Not suitable | | 14 | [GSE1142](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1142) | Inflammatory bowel disease (HG-U133B) | 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.; 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=GSE1142) | Not suitable | | 15 | [GSE114527](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE114527) | A systems biology approach identifies ANP32E and other biomarkers of glucocorticoid refractoriness in ulcerative colitis [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=GSE114527) | Not suitable | | 16 | [GSE114591](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE114591) | A systems biology approach identifies ANP32E and other biomarkers of glucocorticoid refractoriness in ulcerative colitis [miRNA-Seq] | 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=GSE114591) | Not suitable | | 17 | [GSE1152](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1152) | Inflammatory bowel disease | none | Disease/model vs control | Biopsy | suitability 0; metadata 100; overall 34 | 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. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1152) | Not suitable | | 18 | [GSE119600](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE119600) | Common functional alterations identified in blood transcriptome of autoimmune cholestatic liver and inflammatory bowel diseases | 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=GSE119600) | Not suitable | | 19 | [GSE126124](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE126124) | Concordance between gene expression in peripheral whole blood and colonic tissue in children with inflammatory bowel disease. | 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=GSE126124) | Not suitable | | 20 | [GSE128682](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE128682) | Transcriptional signatures that define Ulcerative Colitis in remission | none | Disease/model vs control | Biopsy | 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=GSE128682) | Not suitable | | 21 | [GSE131359](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131359) | Differential pathogenic Th17 profile in mesenteric lymph nodes of Crohn's disease and ulcerative colitis patients | 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=GSE131359) | Not suitable | | 22 | [GSE131911](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131911) | Expression Profiles of Circular RNAs in colon biopsies from Crohn’s Disease Patients by Microarray Analysis | 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.; 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=GSE131911) | Not suitable | | 23 | [GSE133060](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE133060) | Gene expression data from a cohort of Chilean Ulcerative Colitis human intestinal samples | 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=GSE133060) | Not suitable | | 24 | [GSE134025](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134025) | Ulcerative colitis gene expressions file | 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=GSE134025) | Not suitable | | 25 | [GSE135223](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135223) | Human macrophage responses to viral-like particles from non-IBD or IBD colonic resections | none | Disease/model vs control | Unclear 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=GSE135223) | Not suitable | | 26 | [GSE137344](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE137344) | Ileum Transcriptomic Profiling in Inflammatory Bowel Disease | none | Disease/model 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=GSE137344) | Not suitable | | 27 | [GSE144521](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE144521) | RNA profiles in serum and urine extracellular vesicles of patients with cholangiocarcinoma mimicking tumor expression: novel liquid biopsy approach | none | Patient biofluid vs healthy control | Biofluid | 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.; EXTRACELLULAR_VESICLE_CONTEXT [warning]: Extracellular vesicle or exosome context was detected and may not represent ordinary tissue bulk RNA-seq.; 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=GSE144521) | Not suitable | | 28 | [GSE14580](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14580) | Mucosal gene signatures to predict response to infliximab in patients with ulcerative colitis | 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.; 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=GSE14580) | Not suitable | | 29 | [GSE155301](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE155301) | Comprehensive transcriptome profiling of ulcerative colitis mouse model suggests biomarkers and therapeutic targets for human colitis [RNA-Seq] | none | Disease/model vs 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.; 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=GSE155301) | Not suitable | | 30 | [GSE15934](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15934) | Analysis of Gene Expression changes in human intestinal endothelial-to-mesenchymal transition - TRANSFORMED GROUP | 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.; 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=GSE15934) | Not suitable | | 31 | [GSE164871](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE164871) | RNA-seq of 4 Crohn's disease and 4 control | 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=GSE164871) | Not suitable | | 32 | [GSE16879](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16879) | Mucosal expression profiling in patients with inflammatory bowel disease before and after first 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=GSE16879) | Not suitable | | 33 | [GSE169568](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE169568) | BeadChip microarray data of peripheral blood obtained from treatment-näive IBD patients and control individuals | 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=GSE169568) | Not suitable | | 34 | [GSE169569](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE169569) | Small RNA-seq data of peripheral blood obtained from treatment-näive IBD patients and control individuals (small RNA-Seq I) | none | Disease/model vs 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.; 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=GSE169569) | Not suitable | | 35 | [GSE169570](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE169570) | Small RNA-seq data of peripheral blood obtained from treatment-receiving IBD patients and control individuals (small RNA-Seq II) | 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.; 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=GSE169570) | Not suitable | | 36 | [GSE1710](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1710) | Expression profiling in inflammatory bowel disease | 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.; 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=GSE1710) | Not suitable | | 37 | [GSE171057](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE171057) | AI-guided use of balanced PPARα/g dual agonist finetunes macrophage responses in inflammatory bowel disease | none | Treatment 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=GSE171057) | Not suitable | | 38 | [GSE172372](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE172372) | Cyclin-dependent kinase 9 is a therapeutic target for anti-TNF resistant inflammatory bowel disease | 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=GSE172372) | Not suitable | | 39 | [GSE173973](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE173973) | RNA-seq in untreated and Cadherin-11 Knockdown Human Intestinal Myofibroblast cells (HIMF) | 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=GSE173973) | Not suitable | | 40 | [GSE174159](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE174159) | Identifying new pronostic markers of IBD | 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.; 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=GSE174159) | Not suitable | | 41 | [GSE17594](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17594) | NOD2 and human ileal gene expression | 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=GSE17594) | Not suitable | | 42 | [GSE177044](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE177044) | Large-scale whole blood RNA-Seq identifies transcriptional differences between primary sclerosing cholangitis and ulcerative colitis  | none | Disease/model vs control | Biofluid | 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=GSE177044) | Not suitable | | 43 | [GSE179285](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE179285) | Embark cross-sectional study of inactive and active lesions from the ileum and colon of inflammatory bowel disease patients | none | Disease/model vs control | Tissue | suitability 0; metadata 100; overall 34 | MIXED_SAMPLE_TYPES [warning]: Multiple sample type labels or exclusion flags were 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=GSE179285) | Not suitable | | 44 | [GSE186507](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE186507) | Blood expression profiling of an adult inflammatory bowel disease cohort | none | Disease/model vs control | Biofluid | suitability 0; metadata 100; overall 34 | none | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE186507) | Not suitable | | 45 | [GSE191328](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE191328) | Longitudinal multi-omics analysis identifies early blood-based predictors of anti-TNF therapy response in inflammatory bowel disease [RNA-Seq] | none | Disease/model vs control | Biofluid | 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=GSE191328) | Not suitable | | 46 | [GSE193330](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE193330) | Elucidation of the liver pathophysiology of COVID-19 patients using liver-on-a-chips | 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=GSE193330) | Not suitable | | 47 | [GSE193677](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE193677) | Biopsy expression profiling of an adult inflammatory bowel disease cohort | none | Disease/model vs control | Mixed 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=GSE193677) | Not suitable | | 48 | [GSE206285](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE206285) | Efficacy and safety of ustekinumab treatment in patients with ulcerative colitis | 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.; 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=GSE206285) | Not suitable | | 49 | [GSE207022](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE207022) | Efficacy and safety of ustekinumab treatment in patients with Crohn's disease | 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.; 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=GSE207022) | Not suitable | | 50 | [GSE208303](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE208303) | RNA-seq for inflamed and non-inflamed mucosa in patients with Crohn's disease | 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=GSE208303) | Not suitable | | 51 | [GSE215924](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE215924) | Small bowel RNA-seq data from patients with Crohn's disease and patients with colon cancer (non-CD controls) | none | Disease/model 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=GSE215924) | Not suitable | | 52 | [GSE224758](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE224758) | Gene expression profiling of colon biopsies from ulcerative colitis patients and healthy volunteers | none | Disease/model vs control | Biopsy | suitability 0; metadata 100; overall 34 | none | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE224758) | Not suitable | | 53 | [GSE22619](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22619) | Genome wide expression data from discordant twins (ulcerative colitis, primary mucosal tissue) | 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=GSE22619) | Not suitable | | 54 | [GSE227376](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE227376) | Transcriptomic analysis reveals the dynamic changes of immune responses during the development of creeping fat in Crohn's disease | none | Disease/model 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=GSE227376) | Not suitable | | 55 | [GSE227747](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE227747) | Transcriptome Profiling of Intact Bowel Wall Reveals that PDE1A and SEMA3D are Possible Markers with Roles in Enteric Smooth Muscle Apoptosis, Proliferative Disorders, and Autonomic Nervous Abnormality in Crohn's Disease. | none | Disease/model 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=GSE227747) | Not suitable | | 56 | [GSE22889](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22889) | Nitric oxide pathway specific gene alterations in inflammatory bowel disease | 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=GSE22889) | Not suitable | | 57 | [GSE23996](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23996) | Treg_Chip_Expression_Profile_Healthy_vs_Crohns_Disease | 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.; 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=GSE23996) | Not suitable | | 58 | [GSE242140](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE242140) | Study of the Role of Pomegranate Juice Ellagitannins in the Modulation of Inflammation in Inflammatory Bowel Disease | 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=GSE242140) | Not suitable | | 59 | [GSE24287](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24287) | Differential early pathogenic changes in human ileal gene expression in Crohn's disease and ulcerative colitis | 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=GSE24287) | Not suitable | | 60 | [GSE26305](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26305) | Genome-wide gene expression analysis for target genes to differentiate patients with intestinal tuberculosis and Crohn’s disease | 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=GSE26305) | Not suitable | | 61 | [GSE277964](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE277964) | Contribution of Stroma to Inflammatory Bowel Disease Progression Revealed in Patient-Derived Human Colon Chips | 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=GSE277964) | Not suitable | | 62 | [GSE280244](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE280244) | Licochalcone B alleviates Crohn’s Disease injury by targeting FTO | 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=GSE280244) | Not suitable | | 63 | [GSE280813](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE280813) | Licochalcone B alleviates Crohn’s Disease injury by targeting FTO [meRIP-seq] | 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=GSE280813) | Not suitable | | 64 | [GSE296485](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE296485) | The RNA-seq of Ulcerative colitis patients and health | none | Disease/model vs control | Biopsy | suitability 0; metadata 100; overall 34 | none | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE296485) | Not suitable | | 65 | [GSE310282](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE310282) | RNAseq of colonic epithelial and lamina propria-derived Tregs | 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=GSE310282) | Not suitable | | 66 | [GSE3365](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3365) | Comparison of PBMCs in Inflammatory Bowel Disease | 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=GSE3365) | Not suitable | | 67 | [GSE33943](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE33943) | Gene expression profiles of pediatric IBD remission 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=GSE33943) | Not suitable | | 68 | [GSE36807](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE36807) | Genome-wide analysis of Crohn's disease and ulcerative colitis biopsy samples. | 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=GSE36807) | Not suitable | | 69 | [GSE37283](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE37283) | Gene Expression Changes in Non-Dysplastic Mucosa from Patients with Ulcerative Colitis Harboring Remote Neoplastic Lesions | 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=GSE37283) | Not suitable | | 70 | [GSE3801](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE3801) | Gene Expression Profiling of Ulcerative Colitis | 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=GSE3801) | Not suitable | | 71 | [GSE4183](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4183) | Inflammation, adenoma and cancer: objective classification of colon biopsy specimens with gene expression signature | 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.; 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=GSE4183) | Not suitable | | 72 | [GSE42911](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE42911) | Expression data in colon mucosa samples from individuals with ulcerative colitis and normal 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.; 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=GSE42911) | Not suitable | | 73 | [GSE46451](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE46451) | Effects of Inflammation and 5-ASA on ex vivo cultured ulcerative colitis biopsies | 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.; 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=GSE46451) | Not suitable | | 74 | [GSE47908](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE47908) | Transcriptional analysis of left-sided colitis, pancolitis and ulcerative colitis-associated dysplasia | 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=GSE47908) | Not suitable | | 75 | [GSE48958](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE48958) | Mucosal gene expression profiling in (un)inflamed colon of patients with ulcerative colitis (UC) | none | Disease/model vs control | Biopsy | 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=GSE48958) | Not suitable | | 76 | [GSE50788](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50788) | Pouch transcriptional differences between UC and FAP indicate altered immune response. | 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=GSE50788) | Not suitable | | 77 | [GSE53306](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53306) | Differential Gene Expression between Active and Quiescent Stages of Ulcerative Colitis: Insights into a Distinctive Pathogenesis Profile | 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=GSE53306) | Not suitable | | 78 | [GSE59071](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59071) | Mucosal gene expression profiling in patients with inflammatory bowel disease | none | Disease/model vs control | Biopsy | suitability 0; metadata 100; overall 34 | MIXED_SAMPLE_TYPES [warning]: Multiple sample type labels or exclusion flags were 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=GSE59071) | Not suitable | | 79 | [GSE65114](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65114) | Expression data from colonic mucosal biopsies from healthy controls and patients with active ulcerative colitis | 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=GSE65114) | Not suitable | | 80 | [GSE66207](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE66207) | mRNA and small RNA associated with Crohn's disease behavior [RNA-Seq] | none | Disease/model vs control | Biopsy | suitability 0; metadata 100; overall 34 | MIXED_SAMPLE_TYPES [warning]: Multiple sample type labels or exclusion flags were detected.; 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=GSE66207) | Not suitable | | 81 | [GSE66208](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE66208) | mRNA and small RNA associated with Crohn's disease behavior [ncRNA-Seq] | none | Disease/model vs control | Biopsy | suitability 0; metadata 100; overall 34 | MIXED_SAMPLE_TYPES [warning]: Multiple sample type labels or exclusion flags were detected.; 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=GSE66208) | Not suitable | | 82 | [GSE66407](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE66407) | Gut biopsies from patients with Crohn's Disease and Ulcerative Colitis and healthy controls | 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=GSE66407) | Not suitable | | 83 | [GSE66545](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE66545) | Gene expression analysis in mesenteric arteries and veins in Crohn's disease compared to controls from nonIBD samples | 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=GSE66545) | Not suitable | | 84 | [GSE66824](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE66824) | Genomic and Clinical Effects Associated with a Relaxation Response Mind-Body Intervention in Patients with Irritable Bowel Syndrome and Inflammatory Bowel Disease | 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=GSE66824) | Not suitable | | 85 | [GSE6731](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6731) | Genome-wide gene expression differences between Crohn’s and ulcerative colitis from endoscopic pinch biopsies: | 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.; 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=GSE6731) | Not suitable | | 86 | [GSE68306](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68306) | miR-193a-3p is a key tumor-suppressor in ulcerative colitis-associated colon cancer and promotes carcinogenesis through regulation of IL17RD. | none | Disease/model vs control | Biopsy | 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. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68306) | Not suitable | | 87 | [GSE70469](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70469) | Expression data from antigen-specific CD4+T cells from peripheral blood of patietns with CD and healthy controls. | 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=GSE70469) | Not suitable | | 88 | [GSE71730](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE71730) | Plasma induced signatures reveal an extracellular milieu possessing an immunoregulatory bias in treatment naïve inflammatory bowel disease | 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.; 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=GSE71730) | Not suitable | | 89 | [GSE72221](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72221) | Characterization of LncRNA BC012900 among long non-coding RNAs differentially expressed in ulcerative colitis | none | Disease/model vs control | Biopsy | 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. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72221) | Not suitable | | 90 | [GSE72780](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72780) | Intestinal epithelial cells from Crohn's Disease patients | 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=GSE72780) | Not suitable | | 91 | [GSE75214](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75214) | Mucosal gene expression profiling in patients with inflammatory bowel disease study | none | Disease/model vs control | Biopsy | suitability 0; metadata 100; overall 34 | MIXED_SAMPLE_TYPES [warning]: Multiple sample type labels or exclusion flags were 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=GSE75214) | Not suitable | | 92 | [GSE75459](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75459) | Plasma Long Noncoding RNA and mRNA Expression Profile of Crohn’s Disease identified by Microarray | none | Disease/model vs 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=GSE75459) | Not suitable | | 93 | [GSE75916](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75916) | Expression data of epithelial organoid cultures generated from intestinal mucosa of non-IBD controls and patients with ulcerative colitis | none | Disease/model vs control | Organoid | suitability 0; metadata 100; overall 34 | MIXED_SAMPLE_TYPES [warning]: Multiple sample type labels or exclusion flags were detected.; ORGANOIDS_INCLUDED [warning]: Organoid samples appear to be included.; 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=GSE75916) | Not suitable | | 94 | [GSE81266](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE81266) | Ileal pouch transcriptomics reveal shared pathogenesis between pouchitis and ulcerative colitis | 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=GSE81266) | Not suitable | | 95 | [GSE83381](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE83381) | Immune-restricted epigenetic reader SP140 maintains macrophage identity and activation states critical to intestinal homeostasis [RNA-seq] | none | Treatment vs control | Biofluid | suitability 0; metadata 100; overall 34 | AMBIGUOUS_SAMPLES_DETECTED [info]: Ambiguous sample metadata was detected in 8 sample(s): GSM2344751 matched "disease status: unknown"; GSM2344752 matched "disease status: unknown"; GSM2344753 matched "disease status: unknown"; additional ambiguous samples omitted. Review these samples before inclusion or manual group assignment.; 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=GSE83381) | Not suitable | | 96 | [GSE83448](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE83448) | Genome-wide transcriptional analysis in intestinal biopsies from Crohn's disease (CD) patients. | 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=GSE83448) | Not suitable | | 97 | [GSE83687](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE83687) | A functional genomics predictive network model identifies regulators of inflammatory bowel disease: Mount Sinai Hospital (MSH) Population Specimen Collection and Profiling of Inflammatory Bowel Disease | 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=GSE83687) | Not suitable | | 98 | [GSE83982](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE83982) | Differentially expressed Transcribed ultraconserved regions (T-UCRs) in Crohn's disease (CD) comparing to normal controls (NC) | 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.; 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=GSE83982) | Not suitable | | 99 | [GSE87466](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87466) | Gene expression profiling of mucosal biopsies from adult patients with moderately to severely active ulcerative colitis | 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.; 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=GSE87466) | Not suitable | | 100 | [GSE90607](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE90607) | Fibrostenotic phenotype of fibroblasts in Crohn's disease is dependent on tissue stiffness and reversed by LOX inhibition | 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=GSE90607) | Not suitable | | 101 | [GSE92415](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE92415) | Characterization of molecular response to Golimumab in Ulcerative Colitis by mucosal biopsy mRNA expression profiling: results from PURSUIT-SC induction study | none | Treatment vs control | Biopsy | 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=GSE92415) | Not suitable | | 102 | [GSE9452](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9452) | Definition of an ulcerative colitis preinflammatory state | 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.; 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=GSE9452) | Not suitable | | 103 | [GSE94648](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE94648) | Expression data from peripheral whole blood of non-IBD controls, CD and UC 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.; 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=GSE94648) | Not suitable | | 104 | [GSE95095](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE95095) | Differential Gene Expression between involved and uninvolved sites of Crohn’s disease: Insights into a Distinctive Pathogenesis Profile | 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=GSE95095) | Not suitable | | 105 | [GSE96665](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE96665) | Integrated analysis Of Biopsies From Inflammatory Bowel Disease Patients Identifies SAA1 As A Link Between Mucosal Microbes With TH17 And TH22 Cells [diseased subjects] | 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.; 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=GSE96665) | Not suitable | | 106 | [GSE100922](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE100922) | Expression data from whole blood in CD patients undergoing HSCT. | 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=GSE100922) | Not suitable | | 107 | [GSE101816](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE101816) | Colonic miR-31 is a molecular stratifier and prognostic determinant of Crohn’s disease [adult] | 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.; SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; 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=GSE101816) | Not suitable | | 108 | [GSE101817](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE101817) | Association between colonic level of microRNA 31 and subtypes of adult and pediatric Crohn's disease [pediatric] | 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.; SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; 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=GSE101817) | Not suitable | | 109 | [GSE107865](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE107865) | PBMC gene expression from Crohn's disease patients before Infliximab therapy. | 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.; 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.; 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=GSE107865) | Not suitable | | 110 | [GSE122618](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE122618) | Circulating miR 218-5p, alone or in combination, predicts corticosteroid failure in ulcerative colitis. Study through computational strategies based on Systems Biology. | 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.; 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=GSE122618) | Not suitable | | 111 | [GSE130038](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE130038) | Elevated colonic mucin expression correlates with extended time to surgery for ulcerative colitis 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.; 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=GSE130038) | Not suitable | | 112 | [GSE150961](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE150961) | Treatment Naïve and Follow-Up Pediatric Ulcerative Colitis Rectal Gene Expression | 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.; 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=GSE150961) | Not suitable | | 113 | [GSE156044](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE156044) | Transcriptomics analysis of mesenteric adipose tissue from Crohn's disease patients and healthy controls [RNA-seq] | 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=GSE156044) | Not suitable | | 114 | [GSE156453](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE156453) | In vivo gene expression profile of human intestinal epithelial cells: from the viewpoint of drug metabolism and pharmacokinetics | 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_SAMPLE_TYPES [warning]: Multiple sample type labels or exclusion flags were detected.; CELL_LINES_INCLUDED [warning]: Cell line samples appear to be included.; 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=GSE156453) | Not suitable | | 115 | [GSE157020](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE157020) | TSG-6 supports fistulizing Crohn’s disease by a mechanoregulated activation of the epithelial-to-mesenchymal transition | 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=GSE157020) | Not suitable | | 116 | [GSE15933](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15933) | Analysis of Gene Expression changes in human intestinal endothelial-to-mesenchymal transition - UNTREATED/CONTROL GROUP | none | Unclear study design | Tissue | suitability 0; metadata 93; 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.; 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=GSE15933) | Not suitable | | 117 | [GSE186963](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE186963) | Whole blood gene expression from infliximab treated Crohn's disease patients at three time points: pre-treatment, two weeks and fourteen weeks post first 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.; 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=GSE186963) | Not suitable | | 118 | [GSE212849](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE212849) | Prediction of Golimumab Response in the PROgECT Phase 2a Open-Label Trial of Patients With Ulcerative Colitis | 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=GSE212849) | Not suitable | | 119 | [GSE215285](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE215285) | Regional transcriptomics and proteomics of DMPK genes in human intestine | 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=GSE215285) | Not suitable | | 120 | [GSE217352](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE217352) | A Blood-based Transcriptomic Signature Stratifies Severe Crohn's disease and Defines Potentially Targetable Therapeutic Pathways | 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.; 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.; 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=GSE217352) | Not suitable | | 121 | [GSE228122](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE228122) | Bulk RNA-seq of whole biopsies and enteroids/colonoids from terminal ileum and rectum of inflammatory bowel disease patients or control subjects | 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_SAMPLE_TYPES [warning]: Multiple sample type labels or exclusion flags were detected.; ORGANOIDS_INCLUDED [warning]: Organoid samples appear to be included.; AMBIGUOUS_SAMPLES_DETECTED [info]: Ambiguous sample metadata was detected in 1 sample(s): GSM7114773 matched "disease state: NA". Review these samples before inclusion or manual group assignment.; 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=GSE228122) | Not suitable | | 122 | [GSE236055](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE236055) | Colonic mucosal gene expression profile associated with neoplastic progression in longstanding ulcerative colitis | 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=GSE236055) | Not suitable | | 123 | [GSE247146](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE247146) | Blood gene expression biomarkers of response to anti-TNF drugs in pediatric patients before initiation of 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=GSE247146) | Not suitable | | 124 | [GSE25220](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25220) | Transcription levels in human colon biopsies in IBS and IBD patients before and after participating in a high red-meat dietary intervention | 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=GSE25220) | Not suitable | | 125 | [GSE25275](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25275) | Gene expression patterns of biopsies from a colonoscopy taken in 2007 of an ulcerative colitis patient infected with Trichuris trichiura | 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=GSE25275) | Not suitable | | 126 | [GSE25276](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25276) | Gene expression patterns of biopsies from a colonoscopy taken in 2008 of an ulcerative colitis patient infected with Trichuris trichiura | 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=GSE25276) | Not suitable | | 127 | [GSE25277](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25277) | Gene expression patterns of biopsies from a colonoscopy taken in 2009 of an ulcerative colitis patient infected with Trichuris trichiura | 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=GSE25277) | Not suitable | | 128 | [GSE268273](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE268273) | Clinical and molecular characterization of steatotic liver disease in the setting of immune-mediated inflammatory diseases | 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=GSE268273) | Not suitable | | 129 | [GSE276395](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE276395) | Gene expression dysregulation in whole blood of patients with C. difficile infection | 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=GSE276395) | Not suitable | | 130 | [GSE279302](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE279302) | eQTL in diseased colon tissue identifies novel target genes associated with IBD | 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=GSE279302) | Not suitable | | 131 | [GSE317503](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE317503) | Reference-guided genome assembly of long non-coding RNA transcripts reveals target genes associated with Crohn’s disease | none | Unclear study design | Tissue | suitability 0; metadata 93; overall 34 | SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; 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=GSE317503) | Not suitable | | 132 | [GSE33078](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE33078) | Comparison of intestinal surface CD3- refractory celiac disease type II (RCDII) cell lines with intestinal surface CD3+ cell lines of non-RCDII patients | none | Unclear study design | Cell line | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; 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.; 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=GSE33078) | Not suitable | | 133 | [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 | | 134 | [GSE46754](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE46754) | Gene expression analysis of omental and mesenteric adipose tissue in Crohn's disease and ulcerative colitis | 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=GSE46754) | Not suitable | | 135 | [GSE69762](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE69762) | Gene expression of human small intestine generated by biopsy specimens | 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=GSE69762) | Not suitable | | 136 | [GSE74265](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE74265) | Gene expression signature and mitochondrial DNA copy number variation in ulcerative colitis 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.; 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=GSE74265) | Not suitable | | 137 | [GSE77013](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE77013) | A long noncoding RNA signature in Ulcerative Colitis | 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=GSE77013) | Not suitable | | 138 | [GSE87465](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE87465) | Gene expression profiling of mucosal biopsies from pediatric patients with moderately to severely active ulcerative colitis | 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=GSE87465) | Not suitable | | 139 | [GSE102524](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE102524) | Inflammatory Bowel Disease-specific alterations in adipose-derived stroma cell transcriptional profiles | none | Disease/model vs control | Tissue | suitability 0; metadata 85; 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=GSE102524) | Not suitable | | 140 | [GSE230539](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE230539) | IPA analysis of CD14-positive monocytes/macrophages from IBD patients and controls | 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=GSE230539) | Not suitable | | 141 | [GSE23552](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23552) | Exon Array Analysis of Asthmatic Chronic Rhinosinusitis with Nasal Polyps | none | Disease/model vs control | Tissue | suitability 0; metadata 85; 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=GSE23552) | Not suitable | | 142 | [GSE69446](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE69446) | Impact of NOD2 Genotype on the Innate Monocyte Transcriptome in Crohn’s Disease | 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.; TREATED_AND_UNTREATED_SAMPLES_MIXED [info]: Treated and untreated samples are both present.; SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; 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=GSE69446) | Not suitable | | 143 | [GSE148233](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE148233) | Macrophages in Crohn’s disease creeping fat are predominantly inflammatory and produce calprotectin | 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.; 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=GSE148233) | Not suitable | | 144 | [GSE150979](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE150979) | Pro- and anti-tumorigenic capacity of immunoproteasomes in shaping the tumor microenvironment | none | Unclear study design | Tissue | suitability 0; metadata 78; 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.; 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=GSE150979) | Not suitable | | 145 | [GSE20941](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20941) | Mediators in Crohn’s disease influence the gene expression profiles of mesenchymal progenitor cells differentiated into the osteoblastic lineage. | 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.; 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=GSE20941) | Not suitable | | 146 | [GSE60083](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60083) | Genome-wide analysis of monocyte derived macrophages from Crohn's Disease patients and controls | none | Unclear study design | Cultured cells | suitability 0; metadata 78; overall 34 | 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=GSE60083) | Not suitable | ## Ranking explanations ### GSE141174 Scores are usable, but sample metadata contains review-only concerns. - Comparison: Tumor vs unmatched normal. Specimen: Tissue. Comparison suitability: 100%. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Colorectal cancer, Crohn's disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 4 publications; 4 DOIs available: PMID 32049988, PMID 38747892, PMID 39661280, PMID 41747601. - Publication context: Allocating colorectal cancer patients to different risk categories by using a five-biomarker mRNA combination in lymph node analysis.. PloS one, 2020. PMID 32049988. DOI 10.1371/journal.pone.0229007. - Publication context: SPINK4 modulates inhibition of glycolysis against colorectal cancer progression.. Biomolecules & biomedicine, 2024. PMID 38747892. DOI 10.17305/bb.2024.10338. - Publication context: E3 Ubiquitination Ligase MYLIP Mediates the NKRF/SLC25A34 Axis to Suppress Malignant Progression in Colorectal Cancer.. Digestive diseases and sciences, 2025. PMID 39661280. DOI 10.1007/s10620-024-08735-9. - 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: colorectal cancer vs control. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Tumor/normal design boosted for patient tissue triage. - COMPARISON_SUITABILITY: Patient tissue or biopsy specimens boosted for tissue comparison 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. - RECOMMENDATION_REASON: Needs manual review: Scores are usable, but sample metadata contains review-only concerns. - 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: ### GSE92472 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: Crohn's disease, Lupus erythematosus, Sjogren syndrome, Systemic lupus erythematosus, Ulcerative colitis. - 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 28420548. - Publication context: Expression of long non-coding RNAs in autoimmunity and linkage to enhancer function and autoimmune disease risk genetic variants.. Journal of autoimmunity, 2017. PMID 28420548. DOI 10.1016/j.jaut.2017.03.014. - 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: ulcerative colitis 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. ### GSE100833 Dataset does not meet the current suitability threshold. - Comparison: Treatment vs control. Specimen: Mixed specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because specimen/source classes are mixed. - 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: Crohn's disease, Inflammatory bowel disease. - 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 32612148, PMID 36685554, PMID 39894009. - Publication context: Novel candidate drugs in anti-tumor necrosis factor refractory Crohn's diseases: in silico study for drug repositioning.. Scientific reports, 2020. PMID 32612148. DOI 10.1038/s41598-020-67801-0. - Publication context: Investigating regulatory patterns of NLRP3 Inflammasome features and association with immune microenvironment in Crohn's disease.. Frontiers in immunology, 2022. PMID 36685554. DOI 10.3389/fimmu.2022.1096587. - Publication context: Blood transcriptomics identifies FEZ1 as a potential biomarker for inflammatory bowel disease.. Computers in biology and medicine, 2025. PMID 39894009. DOI 10.1016/j.compbiomed.2025.109742. - 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: inflamed tissue 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: 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 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: 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: ### GSE102133 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: Crohn's disease. - Processed data is available for downstream review. - External evidence: Expression Atlas curated experiment link is available. - External evidence: PubMed links 9 publications; 9 DOIs available: PMID 30657881, PMID 36118873, PMID 36714107, PMID 36742294, PMID 38274342. - Publication context: Gene and Mirna Regulatory Networks During Different Stages of Crohn's Disease.. Journal of Crohn's & colitis, 2019. PMID 30657881. DOI 10.1093/ecco-jcc/jjz007. - Publication context: Identifying hub genes and miRNAs in Crohn's disease by bioinformatics analysis.. Frontiers in genetics, 2022. PMID 36118873. DOI 10.3389/fgene.2022.950136. - Publication context: Analysis of ferroptosis-associated genes in Crohn's disease based on bioinformatics.. Frontiers in medicine, 2022. PMID 36714107. DOI 10.3389/fmed.2022.1058076. - 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: Crohn's disease 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: 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: ### GSE10616 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: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 7 publications; 7 DOIs available: PMID 18758464, PMID 29401083, PMID 36479126, PMID 36860851, PMID 37275904. - Publication context: Loci on 20q13 and 21q22 are associated with pediatric-onset inflammatory bowel disease.. Nature genetics, 2008. PMID 18758464. DOI 10.1038/ng.203. - Publication context: Molecular Comparison of Adult and Pediatric Ulcerative Colitis Indicates Broad Similarity of Molecular Pathways in Disease Tissue.. Journal of pediatric gastroenterology and nutrition, 2018. PMID 29401083. DOI 10.1097/MPG.0000000000001898. - Publication context: Integrated analysis of multiple microarray studies to establish differential diagnostic models of Crohn's disease and ulcerative colitis based on a metalloproteinase-associated module.. Frontiers in immunology, 2022. PMID 36479126. DOI 10.3389/fimmu.2022.1022850. - Publication context: 4 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: Crohn's disease 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: ### GSE107499 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: Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 10 publications; 10 DOIs available: PMID 32566650, PMID 32871953, PMID 34997010, PMID 36742294, PMID 37842511. - Publication context: SLC1A1, SLC16A9, and CNTN3 Are Potential Biomarkers for the Occurrence of Colorectal Cancer.. BioMed research international, 2020. PMID 32566650. DOI 10.1155/2020/1204605. - Publication context: Lymphocyte infiltration and key differentially expressed genes in the ulcerative colitis.. Medicine, 2020. PMID 32871953. DOI 10.1097/MD.0000000000021997. - Publication context: Integrated bioinformatics and network pharmacology to identify the therapeutic target and molecular mechanisms of Huangqin decoction on ulcerative Colitis.. Scientific reports, 2022. PMID 34997010. DOI 10.1038/s41598-021-03980-8. - Publication context: 7 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: lesional tissue 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. - 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: ### GSE10791 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: Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 18835392. - Publication context: MicroRNAs are differentially expressed in ulcerative colitis and alter expression of macrophage inflammatory peptide-2 alpha.. Gastroenterology, 2008. PMID 18835392. DOI 10.1053/j.gastro.2008.07.068. - 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: ulcerative colitis 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: 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 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: ### GSE110186 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: Crohn's disease. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 29568200. - Publication context: NOD2- and disease-specific gene expression profiles of peripheral blood mononuclear cells from Crohn's disease patients.. World journal of gastroenterology, 2018. PMID 29568200. DOI 10.3748/wjg.v24.i11.1196. - 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 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. - 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 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: 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: ### GSE111889 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Biopsy. Comparison suitability: 0%. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 3 publications; 3 DOIs available: PMID 31142855, PMID 33769280, PMID 35795659. - Publication context: Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases.. Nature, 2019. PMID 31142855. DOI 10.1038/s41586-019-1237-9. - Publication context: Microbial genetic and transcriptional contributions to oxalate degradation by the gut microbiota in health and disease.. eLife, 2021. PMID 33769280. DOI 10.7554/eLife.63642. - Publication context: Neutrophil Infiltration Characterized by Upregulation of S100A8, S100A9, S100A12 and CXCR2 Is Associated With the Co-Occurrence of Crohn's Disease and Peripheral Artery Disease.. Frontiers in immunology, 2022. PMID 35795659. DOI 10.3389/fimmu.2022.896645. - 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: Crohn's disease vs non-inflamed 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. - 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: ### GSE112057 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. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: recount3 reports trusted processed count availability. - External evidence: Expression Atlas curated experiment link is available. - External evidence: PubMed links 3 publications; 3 DOIs available: PMID 29950172, PMID 34336925, PMID 39894009. - Publication context: Disease-specific regulation of gene expression in a comparative analysis of juvenile idiopathic arthritis and inflammatory bowel disease.. Genome medicine, 2018. PMID 29950172. DOI 10.1186/s13073-018-0558-x. - Publication context: Identification of Key Biomarkers and Immune Infiltration in Systemic Juvenile Idiopathic Arthritis by Integrated Bioinformatic Analysis.. Frontiers in molecular biosciences, 2021. PMID 34336925. DOI 10.3389/fmolb.2021.681526. - Publication context: Blood transcriptomics identifies FEZ1 as a potential biomarker for inflammatory bowel disease.. Computers in biology and medicine, 2025. PMID 39894009. DOI 10.1016/j.compbiomed.2025.109742. - 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: Crohn's disease 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. - 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 biofluid cohort. ### GSE11223 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: Asthma, Breast cancer, Colorectal cancer, Crohn's disease, Inflammatory bowel disease, Prostate cancer, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 4 publications; 4 DOIs available: PMID 18523026, PMID 25822611, PMID 37529244, PMID 39596612. - Publication context: Regional variation in gene expression in the healthy colon is dysregulated in ulcerative colitis.. Gut, 2008. PMID 18523026. DOI 10.1136/gut.2008.148395. - Publication context: Human gastroenteropancreatic expression of melatonin and its receptors MT1 and MT2.. PloS one, 2015. PMID 25822611. DOI 10.1371/journal.pone.0120195. - Publication context: Analysis of cuproptosis-related genes in Ulcerative colitis and immunological characterization based on machine learning.. Frontiers in medicine, 2023. PMID 37529244. DOI 10.3389/fmed.2023.1115500. - 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: treated vs mixed controls. - 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. - 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: 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. - MIXED_SAMPLE_TYPES [WARNING]: Multiple sample type labels or exclusion flags were detected.; samples: - TREATED_SAMPLES_NEED_REVIEW [INFO]: Treated samples may need review depending on the comparison.; samples: GSM282928, GSM282929, GSM282930, GSM282931, GSM282932, GSM282933, GSM282934, GSM282935, GSM282936, GSM282937, GSM282938, GSM282939, GSM282940, GSM282941, GSM282942, GSM282943, GSM282944, GSM282945, GSM282946, GSM282947, GSM282948, GSM282949, GSM282950, GSM282951, GSM282952, GSM282953, GSM282954, GSM282955, GSM282956, GSM282957, GSM282958, GSM282959, GSM282960, GSM282961, GSM282962, GSM282963, GSM282964, GSM282965, GSM282966, GSM282967, GSM282968, GSM282969, GSM282970, GSM282971, GSM282972, GSM282973, GSM282974, GSM282975, GSM282976, GSM282977, GSM282978, GSM282979, GSM282980, GSM282981, GSM282982, GSM282983, GSM282984, GSM282985, GSM282986, GSM282987, GSM282988, GSM282989, GSM282990, GSM282991, GSM282992, GSM282993, GSM282994, GSM282995, GSM282996, GSM282997, GSM282998, GSM282999, GSM283000, GSM283001, GSM283002, GSM283003, GSM283004, GSM283005, GSM283006, GSM283007, GSM283008, GSM283009, GSM283010, GSM283011, GSM283012, GSM283013, GSM283014, GSM283015, GSM283016, GSM283017, GSM283018, GSM283019, GSM283020, GSM283021, GSM283022, GSM283023, GSM283024, GSM283025, GSM283026, GSM283027, GSM283028, GSM283029, GSM283030, GSM283031, GSM283032, GSM283033, GSM283034, GSM283035, GSM283036, GSM283037, GSM283038, GSM283039, GSM283040, GSM283041, GSM283042, GSM283043, GSM283044, GSM283045, GSM283046, GSM283047, GSM283048, GSM283049, GSM283050, GSM283051, GSM283052, GSM283053, GSM283054, GSM283055, GSM283056 - 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: ### GSE112366 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: Crohn's disease, Inflammatory bowel disease. - Processed data is available for downstream review. - External evidence: PubMed links 10 publications; 10 DOIs available: PMID 29782846, PMID 34469062, PMID 36817485, PMID 38521905, PMID 38840917. - Publication context: Abnormal Small Intestinal Epithelial Microvilli in Patients With Crohn's Disease.. Gastroenterology, 2018. PMID 29782846. DOI 10.1053/j.gastro.2018.05.028. - Publication context: Machine learning gene expression predicting model for ustekinumab response in patients with Crohn's disease.. Immunity, inflammation and disease, 2021. PMID 34469062. DOI 10.1002/iid3.506. - Publication context: Identification of immune related gene signature for predicting prognosis of cholangiocarcinoma patients.. Frontiers in immunology, 2023. PMID 36817485. DOI 10.3389/fimmu.2023.1028404. - Publication context: 7 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: treated vs healthy 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: 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 treatment/control experiment. - 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: ### GSE1141 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: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - 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: Crohn's disease 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 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 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: ### GSE1142 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: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 39331894. - Publication context: Characterization of growth arrest-specific transcript 5 and growth arrest-specific transcript 5-related m6A gene signature in glioma: An observational study.. Medicine, 2024. PMID 39331894. DOI 10.1097/MD.0000000000039414. - 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: inflammatory bowel disease 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 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 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: ### GSE114527 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: Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 30329026, PMID 35705632. - Publication context: ANP32E, a Protein Involved in Steroid-Refractoriness in Ulcerative Colitis, Identified by a Systems Biology Approach.. Journal of Crohn's & colitis, 2019. PMID 30329026. DOI 10.1093/ecco-jcc/jjy171. - Publication context: Identification of useful genes from multiple microarrays for ulcerative colitis diagnosis based on machine learning methods.. Scientific reports, 2022. PMID 35705632. DOI 10.1038/s41598-022-14048-6. - 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: ulcerative colitis 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. - 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 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: ### GSE114591 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: Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 30329026. - Publication context: ANP32E, a Protein Involved in Steroid-Refractoriness in Ulcerative Colitis, Identified by a Systems Biology Approach.. Journal of Crohn's & colitis, 2019. PMID 30329026. DOI 10.1093/ecco-jcc/jjy171. - 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: ulcerative colitis 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: 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 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: ### GSE1152 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: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data availability is missing or unclear. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 17058067, PMID 17461471. - Publication context: Aberrant intestinal expression and allelic variants of mucin genes associated with inflammatory bowel disease.. Journal of molecular medicine (Berlin, Germany), 2006. PMID 17058067. DOI 10.1007/s00109-006-0100-2. - Publication context: Aquaporin-8 expression is reduced in ileum and induced in colon of patients with ulcerative colitis.. World journal of gastroenterology, 2007. PMID 17461471. DOI 10.3748/wjg.v13.i11.1687. - 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: Crohn's disease 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 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. - 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. - MISSING_METADATA: Missing or unclear metadata. Processed data availability is missing or unclear. - DOWNGRADE_REASON: Publication context: Aquaporin-8 expression is reduced in ileum and induced in colon of patients with ulcerative colitis.. World journal of gastroenterology, 2007. PMID 17461471. DOI 10.3748/wjg.v13.i11.1687. - 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. - 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: ### GSE119600 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: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 13 publications; 13 DOIs available: PMID 31076612, PMID 34545326, PMID 35741659, PMID 37784152, PMID 37844121. - Publication context: Common functional alterations identified in blood transcriptome of autoimmune cholestatic liver and inflammatory bowel diseases.. Scientific reports, 2019. PMID 31076612. DOI 10.1038/s41598-019-43699-1. - Publication context: Whole Exome Sequencing Identifies Two Novel Mutations in a Patient with UC Associated with PSC and SSA.. Canadian journal of gastroenterology & hepatology, 2021. PMID 34545326. DOI 10.1155/2021/9936932. - Publication context: Exploration of the Common Gene Characteristics and Molecular Mechanism of Parkinson's Disease and Crohn's Disease from Transcriptome Data.. Brain sciences, 2022. PMID 35741659. DOI 10.3390/brainsci12060774. - 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: Case and control sample groups detected: Crohn's disease 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: ### GSE126124 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: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 12 publications; 11 DOIs available: PMID 31618209, PMID 33585004, PMID 34592880, PMID 34786719, PMID 36792688. - Publication context: Concordance between gene expression in peripheral whole blood and colonic tissue in children with inflammatory bowel disease.. PloS one, 2019. PMID 31618209. DOI 10.1371/journal.pone.0222952. - Publication context: Introducing GATA3 as a prominent player in Crohn's disease.. Gastroenterology and hepatology from bed to bench, 2020. PMID 33585004. - Publication context: Evidence for the butyrate metabolism as key pathway improving ulcerative colitis in both pediatric and adult patients.. Bioengineered, 2021. PMID 34592880. DOI 10.1080/21655979.2021.1985815. - Publication context: 9 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: Crohn's disease 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. - 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: ### GSE128682 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Biopsy. Comparison suitability: 0%. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 3 publications; 3 DOIs available: PMID 32322884, PMID 37199828, PMID 38514698. - Publication context: Transcriptional Signatures That Define Ulcerative Colitis in Remission.. Inflammatory bowel diseases, 2021. PMID 32322884. DOI 10.1093/ibd/izaa075. - Publication context: Anti-apoptotic genes and non-coding RNAs are potential outcome predictors for ulcerative colitis.. Functional & integrative genomics, 2023. PMID 37199828. DOI 10.1007/s10142-023-01099-9. - Publication context: DNA methylation fine-tunes pro-and anti-inflammatory signalling pathways in inactive ulcerative colitis tissue biopsies.. Scientific reports, 2024. PMID 38514698. DOI 10.1038/s41598-024-57440-0. - 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: remission 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. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - 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: ### GSE131359 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: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 31191543. - Publication context: Differential Pathogenic Th17 Profile in Mesenteric Lymph Nodes of Crohn's Disease and Ulcerative Colitis Patients.. Frontiers in immunology, 2019. PMID 31191543. DOI 10.3389/fimmu.2019.01177. - 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: Crohn's disease 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: 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: ### GSE131911 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: Crohn's disease, Ulcerative colitis. - 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: ulcerative colitis 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. - 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 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: 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: - 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: ### GSE133060 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, Ulcerative colitis. - 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: Inflamed and non-inflamed sample groups detected. - 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. - 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 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: ### GSE134025 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: Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 4 publications; 3 DOIs available: PMID 32015337, PMID 34925026, PMID 36631011, PMID 39993549. - Publication context: Ferroptosis involves in intestinal epithelial cell death in ulcerative colitis.. Cell death & disease, 2020. PMID 32015337. DOI 10.1038/s41419-020-2299-1. - Publication context: Identification of Pharmacological Autophagy Regulators of Active Ulcerative Colitis.. Frontiers in pharmacology, 2021. PMID 34925026. DOI 10.3389/fphar.2021.769718. - Publication context: [Bioinformatic analysis of molecular mechanism of IL-17 in regulating ulcerative colitis].. Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology, 2023. PMID 36631011. - 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: ulcerative colitis 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. - 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 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: ### GSE135223 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: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 35394816. - Publication context: Human enteric viruses autonomously shape inflammatory bowel disease phenotype through divergent innate immunomodulation.. Science immunology, 2022. PMID 35394816. DOI 10.1126/sciimmunol.abn6660. - 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: Crohn's disease 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: 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. - 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: ### GSE137344 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: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 32058087, PMID 40808866. - Publication context: African Ancestry Proportion Influences Ileal Gene Expression in Inflammatory Bowel Disease.. Cellular and molecular gastroenterology and hepatology, 2020. PMID 32058087. DOI 10.1016/j.jcmgh.2020.02.001. - Publication context: Identifying inflammatory bowel disease subtypes: a comprehensive exploration of transcriptomic data and machine learning-based approaches.. Therapeutic advances in gastroenterology, 2025. PMID 40808866. DOI 10.1177/17562848251362391. - 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: ulcerative colitis 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. - 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: ### GSE144521 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: Other non-gastrointestinal cancer, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 32183400. - Publication context: Patients with Cholangiocarcinoma Present Specific RNA Profiles in Serum and Urine Extracellular Vesicles Mirroring the Tumor Expression: Novel Liquid Biopsy Biomarkers for Disease Diagnosis.. Cells, 2020. PMID 32183400. DOI 10.3390/cells9030721. - 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: ulcerative colitis vs healthy control. - COMPARISON_SUITABILITY: Excluded sample type flags reduce suitability. - DOWNGRADE_REASON: Excluded sample type flags reduce suitability. - 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: 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. - 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. - 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 secondary RNA assays are not primary mRNA tissue RNA-seq. - DOWNGRADE_REASON: Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq. - 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: 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: EXTRACELLULAR_VESICLE_CONTEXT [warning]: Extracellular vesicle or exosome context was detected and may not represent ordinary tissue bulk RNA-seq. - 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. - 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: GSM4290026, GSM4290027, GSM4290028, GSM4290029, GSM4290030, GSM4290031, GSM4290032, GSM4290033, GSM4290034, GSM4290035, GSM4290036, GSM4290037, GSM4290038, GSM4290039, GSM4290040, GSM4290041 - EXTRACELLULAR_VESICLE_CONTEXT [WARNING]: Extracellular vesicle or exosome context was detected and may not represent ordinary tissue bulk RNA-seq.; 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: ### GSE14580 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: Ulcerative colitis. - Processed data is available for downstream review. - External evidence: Expression Atlas curated experiment link is available. - External evidence: PubMed links 7 publications; 7 DOIs available: PMID 19700435, PMID 31886172, PMID 35102110, PMID 35876170, PMID 36983834. - Publication context: Mucosal gene signatures to predict response to infliximab in patients with ulcerative colitis.. Gut, 2009. PMID 19700435. DOI 10.1136/gut.2009.178665. - Publication context: Tenascin-C Is Increased in Inflammatory Bowel Disease and Is Associated with response to Infliximab Therapy.. BioMed research international, 2019. PMID 31886172. DOI 10.1155/2019/1475705. - Publication context: SPP1 in infliximab resistant ulcerative colitis and associated colorectal cancer: an analysis of differentially expressed genes.. European journal of gastroenterology & hepatology, 2022. PMID 35102110. DOI 10.1097/MEG.0000000000002349. - Publication context: 4 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: ulcerative colitis 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: 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: ### GSE155301 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. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Inflammatory bowel disease, Ulcerative colitis. - 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: ulcerative colitis 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: 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 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 secondary RNA assays are not primary mRNA tissue RNA-seq. - DOWNGRADE_REASON: Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - 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. - WARNING_CODE: INTENT_ASSAY_MISMATCH [critical]: Dataset organism does not match the human patient-tissue tumor-normal intent. - SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: - INTENT_ASSAY_MISMATCH [CRITICAL]: Dataset organism does not match the human patient-tissue tumor-normal intent.; samples: ### GSE15934 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: Crohn's disease, Fibrosis, Inflammatory bowel disease, Ulcerative colitis. - 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: ulcerative colitis 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: 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 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: 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: - 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: ### GSE164871 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: Crohn's disease. - 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: Crohn's disease 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. - 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. ### GSE16879 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: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - 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 19956723, PMID 34650991, PMID 34775094, PMID 35876170, PMID 36685554. - Publication context: Mucosal gene expression of antimicrobial peptides in inflammatory bowel disease before and after first infliximab treatment.. PloS one, 2009. PMID 19956723. DOI 10.1371/journal.pone.0007984. - Publication context: Novel Gene Signatures Predicting Primary Non-response to Infliximab in Ulcerative Colitis: Development and Validation Combining Random Forest With Artificial Neural Network.. Frontiers in medicine, 2021. PMID 34650991. DOI 10.3389/fmed.2021.678424. - Publication context: Potential Pathogenic Genes and Mechanism of Ankylosing Spondylitis: A Study Based on WGCNA and Bioinformatics Analysis.. World neurosurgery, 2022. PMID 34775094. DOI 10.1016/j.wneu.2021.11.014. - 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: ulcerative colitis 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: 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: ### GSE169568 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: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 7 publications; 7 DOIs available: PMID 35022690, PMID 39252244, PMID 39894009, PMID 39931173, PMID 40224483. - Publication context: Detailed Transcriptional Landscape of Peripheral Blood Points to Increased Neutrophil Activation in Treatment-Naïve Inflammatory Bowel Disease.. Journal of Crohn's & colitis, 2022. PMID 35022690. DOI 10.1093/ecco-jcc/jjac003. - Publication context: Identification and validation of coagulation and fibrinolytic-related diagnostic biomarkers for ulcerative colitis by bioinformatics analysis.. Medicine, 2024. PMID 39252244. DOI 10.1097/MD.0000000000039552. - Publication context: Blood transcriptomics identifies FEZ1 as a potential biomarker for inflammatory bowel disease.. Computers in biology and medicine, 2025. PMID 39894009. DOI 10.1016/j.compbiomed.2025.109742. - Publication context: 4 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: ulcerative colitis 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: 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: ### GSE169569 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. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 35022690. - Publication context: Detailed Transcriptional Landscape of Peripheral Blood Points to Increased Neutrophil Activation in Treatment-Naïve Inflammatory Bowel Disease.. Journal of Crohn's & colitis, 2022. PMID 35022690. DOI 10.1093/ecco-jcc/jjac003. - 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: ulcerative colitis 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: 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 secondary RNA assays are not primary mRNA tissue RNA-seq. - DOWNGRADE_REASON: Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - 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. - 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. - SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; 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: ### GSE169570 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. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 35022690. - Publication context: Detailed Transcriptional Landscape of Peripheral Blood Points to Increased Neutrophil Activation in Treatment-Naïve Inflammatory Bowel Disease.. Journal of Crohn's & colitis, 2022. PMID 35022690. DOI 10.1093/ecco-jcc/jjac003. - 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: ulcerative colitis 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: 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 secondary RNA assays are not primary mRNA tissue RNA-seq. - DOWNGRADE_REASON: Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - 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. - 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. - SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; 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: ### GSE1710 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: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 16107186. - Publication context: Dissection of the inflammatory bowel disease transcriptome using genome-wide cDNA microarrays.. PLoS medicine, 2005. PMID 16107186. DOI 10.1371/journal.pmed.0020199. - 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: Crohn's disease 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. - 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: 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: ### GSE171057 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: Experimental colitis, Infectious disease or host response, Inflammatory bowel disease. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 35288651. - Publication context: Artificial intelligence-rationalized balanced PPARα/γ dual agonism resets dysregulated macrophage processes in inflammatory bowel disease.. Communications biology, 2022. PMID 35288651. DOI 10.1038/s42003-022-03168-4. - 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 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. - 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: 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: ### GSE172372 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: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 35660024. - Publication context: Cyclin-dependent Kinase 9 as a Potential Target for Anti-TNF-resistant Inflammatory Bowel Disease.. Cellular and molecular gastroenterology and hepatology, 2022. PMID 35660024. DOI 10.1016/j.jcmgh.2022.05.011. - 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. - 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: ### GSE173973 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: Crohn's disease. - 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: Crohn's disease 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: 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. ### GSE174159 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. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 36175116, PMID 38558943. - Publication context: Harnessing the Vnn1 pantetheinase pathway boosts short chain fatty acids production and mucosal protection in colitis.. Gut, 2023. PMID 36175116. DOI 10.1136/gutjnl-2021-325792. - Publication context: Shared Immune Associations Between COVID-19 and Inflammatory Bowel Disease: A Cross-Sectional Observational Study in Shanghai, China.. Journal of inflammation research, 2024. PMID 38558943. DOI 10.2147/JIR.S449746. - 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 mixed controls. - 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. - 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: TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison. - 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. - TREATED_SAMPLES_NEED_REVIEW [INFO]: Treated samples may need review depending on the comparison.; samples: GSM5288086, GSM5288090, GSM5288094, GSM5288097, GSM5288098, GSM5288099 - 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: ### GSE17594 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: Crohn's disease. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 20155851. - Publication context: NOD2 status and human ileal gene expression.. Inflammatory bowel diseases, 2010. PMID 20155851. DOI 10.1002/ibd.21208. - 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: Crohn's disease 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: 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: ### GSE177044 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. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 3 publications; 3 DOIs available: PMID 38304234, PMID 40565156, PMID 41512512. - Publication context: Whole blood RNA sequencing identifies transcriptional differences between primary sclerosing cholangitis and ulcerative colitis.. JHEP reports : innovation in hepatology, 2024. PMID 38304234. DOI 10.1016/j.jhepr.2023.100988. - Publication context: Exploring the Clinical Implication of S100A9 in Ulcerative Colitis and Its Progression to Cancer: A Journey from Inflammation to Cancer.. International journal of molecular sciences, 2025. PMID 40565156. DOI 10.3390/ijms26125693. - Publication context: Long non-coding RNAs in human peripheral blood as biomarkers for age prediction.. Forensic science international. Genetics, 2026. PMID 41512512. DOI 10.1016/j.fsigen.2025.103419. - 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: ulcerative colitis 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. - 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 biofluid cohort. - 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: ### GSE179285 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: Crohn's disease, Infectious disease or host response, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 21 publications; 21 DOIs available: PMID 34561227, PMID 36479126, PMID 36792688, PMID 37370003, PMID 37904419. - Publication context: Regulation and Role of αE Integrin and Gut Homing Integrins in Migration and Retention of Intestinal Lymphocytes during Inflammatory Bowel Disease.. Journal of immunology (Baltimore, Md. : 1950), 2021. PMID 34561227. DOI 10.4049/jimmunol.2100220. - Publication context: Integrated analysis of multiple microarray studies to establish differential diagnostic models of Crohn's disease and ulcerative colitis based on a metalloproteinase-associated module.. Frontiers in immunology, 2022. PMID 36479126. DOI 10.3389/fimmu.2022.1022850. - Publication context: Integrated multiple microarray studies by robust rank aggregation to identify immune-associated biomarkers in Crohn's disease based on three machine learning methods.. Scientific reports, 2023. PMID 36792688. DOI 10.1038/s41598-022-26345-1. - 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: inflamed tissue 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. - 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: MIXED_SAMPLE_TYPES [warning]: Multiple sample type labels or exclusion flags were 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. - MIXED_SAMPLE_TYPES [WARNING]: Multiple sample type labels or exclusion flags were 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: ### GSE186507 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. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 4 publications; 4 DOIs available: PMID 36109152, PMID 37204242, PMID 38558943, PMID 40808866. - Publication context: Biopsy and blood-based molecular biomarker of inflammation in IBD.. Gut, 2023. PMID 36109152. DOI 10.1136/gutjnl-2021-326451. - Publication context: EPOR activation attenuates colitis via enhancing LC3B-dependent apoptotic cell clearance.. Immunology, 2025. PMID 37204242. DOI 10.1111/imm.13660. - Publication context: Shared Immune Associations Between COVID-19 and Inflammatory Bowel Disease: A Cross-Sectional Observational Study in Shanghai, China.. Journal of inflammation research, 2024. PMID 38558943. DOI 10.2147/JIR.S449746. - 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: ulcerative colitis 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. - 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 biofluid cohort. ### GSE191328 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. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 4 publications; 4 DOIs available: PMID 36153599, PMID 38022524, PMID 39444028, PMID 40280281. - Publication context: Longitudinal multi-omics analysis identifies early blood-based predictors of anti-TNF therapy response in inflammatory bowel disease.. Genome medicine, 2022. PMID 36153599. DOI 10.1186/s13073-022-01112-z. - Publication context: The SYSCID map: a graphical and computational resource of molecular mechanisms across rheumatoid arthritis, systemic lupus erythematosus and inflammatory bowel disease.. Frontiers in immunology, 2023. PMID 38022524. DOI 10.3389/fimmu.2023.1257321. - Publication context: Hexokinase 2 expression in apical enterocytes correlates with inflammation severity in patients with inflammatory bowel disease.. BMC medicine, 2024. PMID 39444028. DOI 10.1186/s12916-024-03710-7. - 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: ulcerative colitis 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: 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. - 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: ### GSE193330 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: COVID-19, Infectious disease or host response, Inflammatory bowel disease. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 36896132. - Publication context: Elucidation of the liver pathophysiology of COVID-19 patients using liver-on-a-chips.. PNAS nexus, 2023. PMID 36896132. DOI 10.1093/pnasnexus/pgad029. - 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: COVID-19 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. - 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: GSM5792285, GSM5792286, GSM5792287, GSM5792288, GSM5792289, GSM5792290, GSM5792291, GSM5792292, GSM5792293, GSM5792294, GSM5792295, GSM5792296 ### GSE193677 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: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 7 publications; 7 DOIs available: PMID 36109152, PMID 38161356, PMID 38510272, PMID 39088353, PMID 40808866. - Publication context: Biopsy and blood-based molecular biomarker of inflammation in IBD.. Gut, 2023. PMID 36109152. DOI 10.1136/gutjnl-2021-326451. - Publication context: APOL1 Induces Pyroptosis of Fibroblasts Through NLRP3/Caspase-1/GSDMD Signaling Pathway in Ulcerative Colitis.. Journal of inflammation research, 2023. PMID 38161356. DOI 10.2147/JIR.S437875. - Publication context: Elucidating the role of TWIST1 in ulcerative colitis: a comprehensive bioinformatics and machine learning approach.. Frontiers in genetics, 2024. PMID 38510272. DOI 10.3389/fgene.2024.1296570. - Publication context: 4 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: ulcerative colitis 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: 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: ### GSE206285 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: Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 11 publications; 11 DOIs available: PMID 36109152, PMID 36170836, PMID 36192482, PMID 38352118, PMID 38800594. - Publication context: Biopsy and blood-based molecular biomarker of inflammation in IBD.. Gut, 2023. PMID 36109152. DOI 10.1136/gutjnl-2021-326451. - Publication context: Cytokine responsive networks in human colonic epithelial organoids unveil a molecular classification of inflammatory bowel disease.. Cell reports, 2022. PMID 36170836. DOI 10.1016/j.celrep.2022.111439. - Publication context: Interleukin-22 regulates neutrophil recruitment in ulcerative colitis and is associated with resistance to ustekinumab therapy.. Nature communications, 2022. PMID 36192482. DOI 10.1038/s41467-022-33331-8. - 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: ulcerative colitis 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: 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: ### GSE207022 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: Crohn's disease, Inflammatory bowel disease. - Processed data is available for downstream review. - External evidence: PubMed links 3 publications; 3 DOIs available: PMID 36170836, PMID 38840917, PMID 38926732. - Publication context: Cytokine responsive networks in human colonic epithelial organoids unveil a molecular classification of inflammatory bowel disease.. Cell reports, 2022. PMID 36170836. DOI 10.1016/j.celrep.2022.111439. - Publication context: Identifying hub genes in response to ustekinumab and the impact of ustekinumab treatment on fibrosis in Crohn's disease.. Frontiers in immunology, 2024. PMID 38840917. DOI 10.3389/fimmu.2024.1401733. - Publication context: Intestinal mRNA expression profiles associated with mucosal healing in ustekinumab-treated Crohn's disease patients: bioinformatics analysis and prospective cohort validation.. Journal of translational medicine, 2024. PMID 38926732. DOI 10.1186/s12967-024-05427-w. - 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: inflamed tissue 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: 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: ### GSE208303 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: Crohn's disease, Inflammatory bowel disease. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 36034703. - Publication context: Reduced diversity of intestinal T-cell receptor repertoire in patients with Crohn's disease.. Frontiers in cellular and infection microbiology, 2022. PMID 36034703. DOI 10.3389/fcimb.2022.932373. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Inflamed and non-inflamed sample groups detected. - 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: Publication context: Reduced diversity of intestinal T-cell receptor repertoire in patients with Crohn's disease.. Frontiers in cellular and infection microbiology, 2022. PMID 36034703. DOI 10.3389/fcimb.2022.932373. ### GSE215924 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: Colorectal cancer, Crohn's disease. - 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: Crohn's disease 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. - 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: ### GSE224758 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Biopsy. Comparison suitability: 0%. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 5 publications; 5 DOIs available: PMID 39144720, PMID 39496592, PMID 39647286, PMID 41485180, PMID 42370017. - Publication context: Predicting novel biomarkers for early diagnosis and dynamic severity monitoring of human ulcerative colitis.. Frontiers in genetics, 2024. PMID 39144720. DOI 10.3389/fgene.2024.1429482. - Publication context: CTLA-4 expressing innate lymphoid cells modulate mucosal homeostasis in a microbiota dependent manner.. Nature communications, 2024. PMID 39496592. DOI 10.1038/s41467-024-51719-6. - Publication context: An Integrative analysis of single-cell RNA-seq, transcriptome and Mendelian randomization for the Identification and validation of NAD(+) Metabolism-Related biomarkers in ulcerative colitis.. International immunopharmacology, 2025. PMID 39647286. DOI 10.1016/j.intimp.2024.113765. - 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: ulcerative colitis 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. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. ### GSE22619 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, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 21621540, PMID 22826509. - Publication context: Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis.. Gastroenterology, 2011. PMID 21621540. DOI 10.1053/j.gastro.2011.04.011. - Publication context: A functional methylome map of ulcerative colitis.. Genome research, 2012. PMID 22826509. DOI 10.1101/gr.138347.112. - 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: ulcerative colitis vs non-inflamed 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: ### GSE227376 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: Colorectal cancer, Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 37594364. - Publication context: Transcriptomic Profiling and Cellular Composition of Creeping Fat in Crohn's disease.. Journal of Crohn's & colitis, 2024. PMID 37594364. DOI 10.1093/ecco-jcc/jjad141. - 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: Crohn's disease 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. - 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: ### GSE227747 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: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 37727374. - Publication context: Transcriptome profiling of intact bowel wall reveals that PDE1A and SEMA3D are possible markers with roles in enteric smooth muscle apoptosis, proliferative disorders, and dysautonomia in Crohn's disease.. Frontiers in genetics, 2023. PMID 37727374. DOI 10.3389/fgene.2023.1194882. - 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: Crohn's disease vs non-inflamed 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. - 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: ### GSE22889 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. - 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: inflammatory bowel disease 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: 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: ### GSE23996 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: Crohn's disease, Inflammatory bowel disease. - 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: Crohn's disease 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. - 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: ### GSE242140 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: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 40255128. - Publication context: Evidence for a Modulatory Effect of a 12-Week Pomegranate Juice Intervention on the Transcriptional Response in Inflammatory Bowel Disease Patients Reducing Fecal Calprotectin Levels: Findings From a Proof-of-Principle Study.. Molecular nutrition & food research, 2025. PMID 40255128. DOI 10.1002/mnfr.70067. - 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: ulcerative colitis vs vehicle 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: 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: 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: ### GSE24287 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: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 5 publications; 5 DOIs available: PMID 22606341, PMID 22719822, PMID 25182475, PMID 36742294, PMID 42269260. - Publication context: An ileal Crohn's disease gene signature based on whole human genome expression profiles of disease unaffected ileal mucosal biopsies.. PloS one, 2012. PMID 22606341. DOI 10.1371/journal.pone.0037139. - Publication context: Host genes related to paneth cells and xenobiotic metabolism are associated with shifts in human ileum-associated microbial composition.. PloS one, 2012. PMID 22719822. DOI 10.1371/journal.pone.0030044. - Publication context: Identifying candidate genes for discrimination of ulcerative colitis and Crohn's disease.. Molecular biology reports, 2014. PMID 25182475. DOI 10.1007/s11033-014-3469-y. - 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: ulcerative colitis 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: 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: ### GSE26305 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: Crohn's disease, Tuberculosis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 25969456. - Publication context: Genome-wide gene expression analysis for target genes to differentiate patients with intestinal tuberculosis and Crohn's disease and discriminative value of FOXP3 mRNA expression.. Gastroenterology report, 2016. PMID 25969456. DOI 10.1093/gastro/gov015. - 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: Crohn's disease 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 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 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: ### GSE277964 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: Crohn's disease, Fibrosis, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 39677416, PMID 39975910. - Publication context: Human Organ Chips Reveal New Inflammatory Bowel Disease Drivers.. medRxiv : the preprint server for health sciences, 2025. PMID 39677416. DOI 10.1101/2024.12.05.24318563. - Publication context: Human Organ Chips Reveal New Inflammatory Bowel Disease Drivers.. Research square, 2025. PMID 39975910. DOI 10.21203/rs.3.rs-5627712/v1. - 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: ulcerative colitis 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. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. ### GSE280244 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: Crohn's disease, Inflammatory bowel disease. - 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: inflammatory bowel disease 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: ### GSE280813 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: Crohn's disease, Inflammatory bowel disease. - 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: inflammatory bowel disease 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. - 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: ### GSE296485 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Biopsy. Comparison suitability: 0%. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Ulcerative colitis. - 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: ulcerative colitis 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. - 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. ### GSE310282 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: Colorectal cancer, Crohn's disease, Inflammatory bowel disease. - 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: Crohn's disease 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. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. ### GSE3365 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: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 11 publications; 11 DOIs available: PMID 16436634, PMID 31618209, PMID 37291580, PMID 39006497, PMID 39712025. - Publication context: Molecular classification of Crohn's disease and ulcerative colitis patients using transcriptional profiles in peripheral blood mononuclear cells.. The Journal of molecular diagnostics : JMD, 2006. PMID 16436634. DOI 10.2353/jmoldx.2006.050079. - Publication context: Concordance between gene expression in peripheral whole blood and colonic tissue in children with inflammatory bowel disease.. PloS one, 2019. PMID 31618209. DOI 10.1371/journal.pone.0222952. - Publication context: Exploring the molecular mechanism of comorbidity of autism spectrum disorder and inflammatory bowel disease by combining multiple data sets.. Journal of translational medicine, 2023. PMID 37291580. DOI 10.1186/s12967-023-04218-z. - 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: ulcerative colitis 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. - 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. - 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: ### GSE33943 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: Inflammatory bowel disease. - Processed data is available for downstream review. - External evidence: PubMed links 3 publications; 3 DOIs available: PMID 24260248, PMID 29381010, PMID 39894009. - Publication context: Gene expression analysis of peripheral cells for subclassification of pediatric inflammatory bowel disease in remission.. PloS one, 2013. PMID 24260248. DOI 10.1371/journal.pone.0079549. - Publication context: Identification of crucial genes of pediatric inflammatory bowel disease in remission by protein-protein interaction network and module analyses.. Minerva pediatrics, 2023. PMID 29381010. DOI 10.23736/S2724-5276.18.04997-6. - Publication context: Blood transcriptomics identifies FEZ1 as a potential biomarker for inflammatory bowel disease.. Computers in biology and medicine, 2025. PMID 39894009. DOI 10.1016/j.compbiomed.2025.109742. - 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: inflammatory bowel disease 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. - 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 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: ### GSE36807 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: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 21 publications; 21 DOIs available: PMID 24155895, PMID 30015893, PMID 32489050, PMID 34717557, PMID 35497913. - Publication context: Identification of novel predictor classifiers for inflammatory bowel disease by gene expression profiling.. PloS one, 2013. PMID 24155895. DOI 10.1371/journal.pone.0076235. - Publication context: Comprehensive analysis of gene expression profiles provides insight into the pathogenesis of Crohn's disease.. Molecular medicine reports, 2018. PMID 30015893. DOI 10.3892/mmr.2018.9267. - Publication context: [Bioinformatic analysis of differentially expressed genes and Chinese medicine prediction for ulcerative colitis].. Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica, 2020. PMID 32489050. DOI 10.19540/j.cnki.cjcmm.20191030.401. - 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: Crohn's disease 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: ### GSE37283 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: Colorectal cancer, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 4 publications; 4 DOIs available: PMID 23388545, PMID 23945234, PMID 34717557, PMID 39071816. - Publication context: Gene signature distinguishes patients with chronic ulcerative colitis harboring remote neoplastic lesions.. Inflammatory bowel diseases, 2013. PMID 23388545. DOI 10.1097/MIB.0b013e3182802bac. - Publication context: Intestinal epithelial vitamin D receptor signaling inhibits experimental colitis.. The Journal of clinical investigation, 2013. PMID 23945234. DOI 10.1172/JCI65842. - Publication context: Screening of characteristic genes in ulcerative colitis by integrating gene expression profiles.. BMC gastroenterology, 2021. PMID 34717557. DOI 10.1186/s12876-021-01940-0. - 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: ulcerative colitis 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: ### GSE3801 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: Ulcerative colitis. - 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: ulcerative colitis 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. - 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: ### GSE4183 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: Colorectal cancer, Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: Expression Atlas curated experiment link is available. - External evidence: PubMed links 12 publications; 12 DOIs available: PMID 18776587, PMID 19461970, PMID 20957034, PMID 23155391, PMID 25405986. - Publication context: Inflammation, adenoma and cancer: objective classification of colon biopsy specimens with gene expression signature.. Disease markers, 2008. PMID 18776587. DOI 10.1155/2008/586721. - Publication context: Evaluation of microarray preprocessing algorithms based on concordance with RT-PCR in clinical samples.. PloS one, 2009. PMID 19461970. DOI 10.1371/journal.pone.0005645. - Publication context: Modeling oncogenic signaling in colon tumors by multidirectional analyses of microarray data directed for maximization of analytical reliability.. PloS one, 2010. PMID 20957034. DOI 10.1371/journal.pone.0013091. - Publication context: 9 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: colorectal cancer 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: ### GSE42911 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: Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 24937444. - Publication context: DNA methylation-associated colonic mucosal immune and defense responses in treatment-naïve pediatric ulcerative colitis.. Epigenetics, 2014. PMID 24937444. DOI 10.4161/epi.29446. - 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: ulcerative colitis 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: 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: ### GSE46451 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: Ulcerative colitis. - 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: Inflamed and non-inflamed sample groups detected. - 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: 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: ### GSE47908 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: Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 17 publications; 17 DOIs available: PMID 25358065, PMID 33987007, PMID 35604388, PMID 36982725, PMID 37056910. - Publication context: Transcriptional analysis of left-sided colitis, pancolitis, and ulcerative colitis-associated dysplasia.. Inflammatory bowel diseases, 2014. PMID 25358065. DOI 10.1097/MIB.0000000000000235. - Publication context: Identification of key genes and biological processes contributing to colitis associated dysplasia in ulcerative colitis.. PeerJ, 2021. PMID 33987007. DOI 10.7717/peerj.11321. - Publication context: Molecular Network Analyses Implicate Death-Associated Protein Kinase 3 (DAPK3) as a Key Factor in Colitis-Associated Dysplasia Progression.. Inflammatory bowel diseases, 2022. PMID 35604388. DOI 10.1093/ibd/izac098. - Publication context: 14 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: ulcerative colitis 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: 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: ### GSE48958 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: Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 12 publications; 11 DOIs available: PMID 25546151, PMID 33144895, PMID 33462173, PMID 33941565, PMID 34939750. - Publication context: Integrated miRNA and mRNA expression profiling in inflamed colon of patients with ulcerative colitis.. PloS one, 2014. PMID 25546151. DOI 10.1371/journal.pone.0116117. - Publication context: Identification of Differential Intestinal Mucosa Transcriptomic Biomarkers for Ulcerative Colitis by Bioinformatics Analysis.. Disease markers, 2020. PMID 33144895. DOI 10.1155/2020/8876565. - Publication context: Bioinformatics Analysis of Differentially Expressed Genes and Protein-Protein Interaction Networks Associated with Functional Pathways in Ulcerative Colitis.. Medical science monitor : international medical journal of experimental and clinical research, 2021. PMID 33462173. DOI 10.12659/MSM.927917. - Publication context: 9 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: inflamed tissue 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. - 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 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: ### GSE50788 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: Ulcerative colitis. - 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: Inflamed and non-inflamed sample groups detected. - 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: 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: ### GSE53306 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, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 10 publications; 10 DOIs available: PMID 26034135, PMID 34925026, PMID 35705632, PMID 37351719, PMID 37529244. - Publication context: Mobilization of epithelial mesenchymal transition genes distinguishes active from inactive lesional tissue in patients with ulcerative colitis.. Human molecular genetics, 2015. PMID 26034135. DOI 10.1093/hmg/ddv192. - Publication context: Identification of Pharmacological Autophagy Regulators of Active Ulcerative Colitis.. Frontiers in pharmacology, 2021. PMID 34925026. DOI 10.3389/fphar.2021.769718. - Publication context: Identification of useful genes from multiple microarrays for ulcerative colitis diagnosis based on machine learning methods.. Scientific reports, 2022. PMID 35705632. DOI 10.1038/s41598-022-14048-6. - Publication context: 7 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: ulcerative colitis 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. - 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: ### GSE59071 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: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: Expression Atlas curated experiment link is available. - External evidence: PubMed links 13 publications; 13 DOIs available: PMID 26313692, PMID 30015893, PMID 33144895, PMID 33686088, PMID 34306038. - Publication context: Strong Upregulation of AIM2 and IFI16 Inflammasomes in the Mucosa of Patients with Active Inflammatory Bowel Disease.. Inflammatory bowel diseases, 2015. PMID 26313692. DOI 10.1097/MIB.0000000000000535. - Publication context: Comprehensive analysis of gene expression profiles provides insight into the pathogenesis of Crohn's disease.. Molecular medicine reports, 2018. PMID 30015893. DOI 10.3892/mmr.2018.9267. - Publication context: Identification of Differential Intestinal Mucosa Transcriptomic Biomarkers for Ulcerative Colitis by Bioinformatics Analysis.. Disease markers, 2020. PMID 33144895. DOI 10.1155/2020/8876565. - 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: Case and control sample groups detected: inflamed tissue 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: MIXED_SAMPLE_TYPES [warning]: Multiple sample type labels or exclusion flags were 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. - MIXED_SAMPLE_TYPES [WARNING]: Multiple sample type labels or exclusion flags were 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: ### GSE65114 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: Ulcerative colitis. - 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 34717557, PMID 37055495, PMID 40428318. - Publication context: Screening of characteristic genes in ulcerative colitis by integrating gene expression profiles.. BMC gastroenterology, 2021. PMID 34717557. DOI 10.1186/s12876-021-01940-0. - Publication context: Identification of hub genes and immune infiltration in ulcerative colitis using bioinformatics.. Scientific reports, 2023. PMID 37055495. DOI 10.1038/s41598-023-33292-y. - Publication context: Development and Experimental Validation of Machine Learning-Based Disulfidptosis-Related Ferroptosis Biomarkers in Inflammatory Bowel Disease.. Genes, 2025. PMID 40428318. DOI 10.3390/genes16050496. - 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: ulcerative colitis 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: 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: ### GSE66207 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Biopsy. Comparison suitability: 0%. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Colorectal cancer, Crohn's disease, Inflammatory bowel disease. - 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 26164662, PMID 34749666, PMID 39169060. - Publication context: MicroRNAs Classify Different Disease Behavior Phenotypes of Crohn's Disease and May Have Prognostic Utility.. Inflammatory bowel diseases, 2015. PMID 26164662. DOI 10.1097/MIB.0000000000000478. - Publication context: An alternative splicing signature in human Crohn's disease.. BMC gastroenterology, 2021. PMID 34749666. DOI 10.1186/s12876-021-02001-2. - Publication context: Identification and multimodal characterization of a specialized epithelial cell type associated with Crohn's disease.. Nature communications, 2024. PMID 39169060. DOI 10.1038/s41467-024-51580-7. - 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: inflamed tissue 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: 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 secondary RNA assays are not primary mRNA tissue RNA-seq. - DOWNGRADE_REASON: Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - WARNING_CODE: MIXED_SAMPLE_TYPES [warning]: Multiple sample type labels or exclusion flags were detected. - WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. - MIXED_SAMPLE_TYPES [WARNING]: Multiple sample type labels or exclusion flags were detected.; samples: - SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: ### GSE66208 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Biopsy. Comparison suitability: 0%. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Colorectal cancer, Crohn's disease, Inflammatory bowel disease. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 26164662. - Publication context: MicroRNAs Classify Different Disease Behavior Phenotypes of Crohn's Disease and May Have Prognostic Utility.. Inflammatory bowel diseases, 2015. PMID 26164662. DOI 10.1097/MIB.0000000000000478. - 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: inflamed tissue 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: 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 secondary RNA assays are not primary mRNA tissue RNA-seq. - DOWNGRADE_REASON: Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - WARNING_CODE: MIXED_SAMPLE_TYPES [warning]: Multiple sample type labels or exclusion flags were detected. - WARNING_CODE: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. - MIXED_SAMPLE_TYPES [WARNING]: Multiple sample type labels or exclusion flags were detected.; samples: - SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; samples: ### GSE66407 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: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 3 publications; 3 DOIs available: PMID 37902927, PMID 38274809, PMID 42288480. - Publication context: Management of ulcerative colitis by dichloroacetate: Impact on NFATC1/NLRP3/IL1B signaling based on bioinformatics analysis combined with in vivo experimental verification.. Inflammopharmacology, 2024. PMID 37902927. DOI 10.1007/s10787-023-01362-2. - Publication context: Construction of a molecular inflammatory predictive model with histone modification-related genes and identification of CAMK2D as a potential response signature to infliximab in ulcerative colitis.. Frontiers in immunology, 2023. PMID 38274809. DOI 10.3389/fimmu.2023.1282136. - Publication context: DsbA-L safeguards T cell mitochondrial redox homeostasis to restrain Th17 differentiation and colitis.. Cell death & disease, 2026. PMID 42288480. DOI 10.1038/s41419-026-08978-6. - 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: inflamed tissue 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: ### GSE66545 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: Crohn's disease. - 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: Crohn's disease 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. - 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: ### GSE66824 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: Inflammatory bowel disease. - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 25927528, PMID 42299241. - Publication context: Genomic and clinical effects associated with a relaxation response mind-body intervention in patients with irritable bowel syndrome and inflammatory bowel disease.. PloS one, 2015. PMID 25927528. DOI 10.1371/journal.pone.0123861. - Publication context: Genomic Research for Abdominal Pain in Patients with Irritable Bowel Syndrome or Inflammatory Bowel Disease Before and After Mind-Body Intervention.. Journal of pain research, 2026. PMID 42299241. DOI 10.2147/JPR.S605236. - 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: inflammatory bowel disease 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: 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: 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: ### GSE6731 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: Crohn's disease, Infectious disease or host response, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: Expression Atlas curated experiment link is available. - External evidence: PubMed links 4 publications; 3 DOIs available: PMID 17262812, PMID 26636514, PMID 35705632, PMID 36118873. - Publication context: Genome-wide gene expression differences in Crohn's disease and ulcerative colitis from endoscopic pinch biopsies: insights into distinctive pathogenesis.. Inflammatory bowel diseases, 2007. PMID 17262812. DOI 10.1002/ibd.20110. - Publication context: Bioinformatic analysis of potential candidates for therapy of inflammatory bowel disease.. European review for medical and pharmacological sciences, 2015. PMID 26636514. - Publication context: Identification of useful genes from multiple microarrays for ulcerative colitis diagnosis based on machine learning methods.. Scientific reports, 2022. PMID 35705632. DOI 10.1038/s41598-022-14048-6. - 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: Crohn's disease 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. - 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: 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: ### GSE68306 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: Colorectal cancer, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 28600480. - Publication context: miR-193a-3p is a Key Tumor Suppressor in Ulcerative Colitis-Associated Colon Cancer and Promotes Carcinogenesis through Upregulation of IL17RD.. Clinical cancer research : an official journal of the American Association for Cancer Research, 2017. PMID 28600480. DOI 10.1158/1078-0432.CCR-17-0171. - 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: ulcerative colitis 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: 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. - 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 secondary RNA assays are not primary mRNA tissue RNA-seq. - DOWNGRADE_REASON: Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq. - 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: 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. - 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: ### GSE70469 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: Crohn's disease, Infectious disease or host response. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 27267052. - Publication context: Commensal-Specific CD4(+) Cells From Patients With Crohn's Disease Have a T-Helper 17 Inflammatory Profile.. Gastroenterology, 2016. PMID 27267052. DOI 10.1053/j.gastro.2016.05.050. - 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: Crohn's disease 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: ### GSE71730 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. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Crohn's disease, Inflammatory bowel disease, Metabolic disease, Type 1 diabetes, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 3 publications; 3 DOIs available: PMID 26660358, PMID 39894009, PMID 42112146. - Publication context: Plasma-induced signatures reveal an extracellular milieu possessing an immunoregulatory bias in treatment-naive paediatric inflammatory bowel disease.. Clinical and experimental immunology, 2016. PMID 26660358. DOI 10.1111/cei.12753. - Publication context: Blood transcriptomics identifies FEZ1 as a potential biomarker for inflammatory bowel disease.. Computers in biology and medicine, 2025. PMID 39894009. DOI 10.1016/j.compbiomed.2025.109742. - Publication context: Aimed at Subtype Discrimination but Yielding a Shared Marker: Integrative Analysis of Blood Transcriptomes Reveals Upregulated TLR5 as a Potential Biomarker for IBD.. Clinical and experimental gastroenterology, 2026. PMID 42112146. DOI 10.2147/CEG.S584999. - 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: Crohn's disease 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: 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. - 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: 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. - 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: GSM1844252, GSM1844253, GSM1844254, GSM1844255, GSM1844256, GSM1844257, GSM1844258, GSM1844259, GSM1844260, GSM1844261, GSM1844262, GSM1844263, GSM1844264, GSM1844265, GSM1844266, GSM1844267, GSM1844268, GSM1844269, GSM1844270, GSM1844271, GSM1844272, GSM1844273, GSM1844274, GSM1844275, GSM1844276, GSM1844277, GSM1844278, GSM1844279, GSM1844280, GSM1844281, GSM1844282, GSM1844283, GSM1844284, GSM1844285, GSM1844286, GSM1844287, GSM1844288, GSM1844289, GSM1844290, GSM1844291, GSM1844292, GSM1844293, GSM1844294, GSM1844295, GSM1844296, GSM1844297, GSM1844298 - TREATED_SAMPLES_NEED_REVIEW [INFO]: Treated samples may need review depending on the comparison.; samples: GSM1844252, GSM1844253, GSM1844254, GSM1844255, GSM1844256, GSM1844257, GSM1844258, GSM1844259, GSM1844260, GSM1844261, GSM1844262, GSM1844263, GSM1844264, GSM1844265, GSM1844266, GSM1844267, GSM1844268, GSM1844269, GSM1844270, GSM1844271, GSM1844272, GSM1844273, GSM1844274, GSM1844275, GSM1844276, GSM1844277, GSM1844278, GSM1844279, GSM1844280, GSM1844281, GSM1844282, GSM1844283, GSM1844284, GSM1844285, GSM1844286, GSM1844287, GSM1844288, GSM1844289, GSM1844290, GSM1844291, GSM1844292, GSM1844293, GSM1844294, GSM1844295, GSM1844296, GSM1844297, GSM1844298 - 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: ### GSE72221 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: Crohn's disease, Infectious disease or host response, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 26937624. - Publication context: Ulcerative Colitis-Associated Long Noncoding RNA, BC012900, Regulates Intestinal Epithelial Cell Apoptosis.. Inflammatory bowel diseases, 2016. PMID 26937624. DOI 10.1097/MIB.0000000000000691. - 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: ulcerative colitis vs mixed controls. - 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 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: 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. - 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: ### GSE72780 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: Crohn's disease, Inflammatory bowel disease. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 26752649. - Publication context: Rho-A prenylation and signaling link epithelial homeostasis to intestinal inflammation.. The Journal of clinical investigation, 2016. PMID 26752649. DOI 10.1172/JCI80997. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Inflamed and non-inflamed sample groups detected. - 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 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 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: ### GSE75214 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: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 21 publications; 21 DOIs available: PMID 28885228, PMID 40645380, PMID 40689397, PMID 40771912, PMID 40901026. - Publication context: Genetic and Transcriptomic Bases of Intestinal Epithelial Barrier Dysfunction in Inflammatory Bowel Disease.. Inflammatory bowel diseases, 2017. PMID 28885228. DOI 10.1097/MIB.0000000000001246. - Publication context: Identification of cholesterol homeostasis related genes and potential pathogenesis mechanisms in ulcerative colitis.. The Journal of steroid biochemistry and molecular biology, 2025. PMID 40645380. DOI 10.1016/j.jsbmb.2025.106833. - Publication context: HMGB1 Exacerbates Intestinal Barrier Damage by Inducing Ferroptosis Through the TLR4/NF-κB/GPX4 Pathway in Ulcerative Colitis.. Mediators of inflammation, 2025. PMID 40689397. DOI 10.1155/mi/2395557. - 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: inflamed tissue 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: MIXED_SAMPLE_TYPES [warning]: Multiple sample type labels or exclusion flags were 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. - MIXED_SAMPLE_TYPES [WARNING]: Multiple sample type labels or exclusion flags were 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: ### GSE75459 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: Crohn's disease. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 27217703. - Publication context: Plasma long noncoding RNA expression profile identified by microarray in patients with Crohn's disease.. World journal of gastroenterology, 2016. PMID 27217703. DOI 10.3748/wjg.v22.i19.4716. - 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: Crohn's disease 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 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: ### GSE75916 Dataset does not meet the current suitability threshold. - Comparison: Disease/model vs control. Specimen: Organoid. 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: Colorectal cancer, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 27803115. - Publication context: Alterations in the epithelial stem cell compartment could contribute to permanent changes in the mucosa of patients with ulcerative colitis.. Gut, 2017. PMID 27803115. DOI 10.1136/gutjnl-2016-312609. - 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: ulcerative colitis 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: 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 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: ORGANOIDS_INCLUDED [warning]: Organoid samples appear to be included. - 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: - ORGANOIDS_INCLUDED [WARNING]: Organoid samples appear to be included.; samples: GSM1970196, GSM1970197, GSM1970198, GSM1970199, GSM1970200, GSM1970201, GSM1970202, GSM1970203, GSM1970204, GSM1970205, GSM1970206, GSM1970207, GSM1970208, GSM1970209, GSM1970210, GSM1970211, GSM1970212, GSM1970213, GSM1970214, GSM1970215, GSM1970216, GSM1970217, GSM1970218, GSM1970219, GSM1970220, GSM1970221, GSM1970222, GSM1970223, GSM1970224, GSM1970225, GSM1970226, GSM1970227, GSM1970228, GSM1970229, GSM1970230, GSM1970231 - 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: ### GSE81266 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: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - 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 28221248. - Publication context: Early Transcriptomic Changes in the Ileal Pouch Provide Insight into the Molecular Pathogenesis of Pouchitis and Ulcerative Colitis.. Inflammatory bowel diseases, 2017. PMID 28221248. DOI 10.1097/MIB.0000000000001027. - 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: ulcerative colitis 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: 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: ### GSE83381 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: Crohn's disease. - Processed data is available for downstream review. - External evidence: recount3 reports trusted processed count availability. - 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: Crohn's disease 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: 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: 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: AMBIGUOUS_SAMPLES_DETECTED [info]: Ambiguous sample metadata was detected in 8 sample(s): GSM2344751 matched "disease status: unknown"; GSM2344752 matched "disease status: unknown"; GSM2344753 matched "disease status: unknown"; additional ambiguous samples omitted. Review these samples before inclusion or manual group assignment. - 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. - AMBIGUOUS_SAMPLES_DETECTED [INFO]: Ambiguous sample metadata was detected in 8 sample(s): GSM2344751 matched "disease status: unknown"; GSM2344752 matched "disease status: unknown"; GSM2344753 matched "disease status: unknown"; additional ambiguous samples omitted. Review these samples before inclusion or manual group assignment.; samples: GSM2344751, GSM2344752, GSM2344753, GSM2344754, GSM2344755, GSM2344756, GSM2344757, GSM2344758 - 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: ### GSE83448 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: Crohn's disease. - Processed data is available for downstream review. - External evidence: PubMed links 3 publications; 3 DOIs available: PMID 32508154, PMID 34628888, PMID 41364644. - Publication context: Transcriptomic identification of TMIGD1 and its relationship with the ileal epithelial cell differentiation in Crohn's disease.. American journal of physiology. Gastrointestinal and liver physiology, 2020. PMID 32508154. DOI 10.1152/ajpgi.00027.2020. - Publication context: Identification and validation of key long non-coding RNAs using co-expression network analysis in Crohn's disease.. Annals of palliative medicine, 2021. PMID 34628888. DOI 10.21037/apm-21-1952. - Publication context: S-palmitoylation-related genes in Crohn's disease: Bioinformatic identification and validation.. Biomolecules & biomedicine, 2025. PMID 41364644. DOI 10.17305/bb.2025.13221. - 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: inflamed tissue vs mixed controls. - 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: 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: ### GSE83687 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: Colorectal cancer, Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: recount3 reports trusted processed count availability. - External evidence: Expression Atlas curated experiment link is available. - External evidence: PubMed links 4 publications; 4 DOIs available: PMID 28892060, PMID 37855835, PMID 38510272, PMID 40179807. - Publication context: A functional genomics predictive network model identifies regulators of inflammatory bowel disease.. Nature genetics, 2017. PMID 28892060. DOI 10.1038/ng.3947. - Publication context: Genetic and dietary modulators of the inflammatory response in the gastrointestinal tract of the BXD mouse genetic reference population.. eLife, 2023. PMID 37855835. DOI 10.7554/eLife.87569. - Publication context: Elucidating the role of TWIST1 in ulcerative colitis: a comprehensive bioinformatics and machine learning approach.. Frontiers in genetics, 2024. PMID 38510272. DOI 10.3389/fgene.2024.1296570. - 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: ulcerative colitis 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. ### GSE83982 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: Crohn's disease. - 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: Crohn's disease 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 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 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: ### GSE87466 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: Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 21 publications; 21 DOIs available: PMID 29401083, PMID 40361222, PMID 40584713, PMID 40600991, PMID 40605290. - Publication context: Molecular Comparison of Adult and Pediatric Ulcerative Colitis Indicates Broad Similarity of Molecular Pathways in Disease Tissue.. Journal of pediatric gastroenterology and nutrition, 2018. PMID 29401083. DOI 10.1097/MPG.0000000000001898. - Publication context: Identifying Lactylation-related biomarkers and therapeutic drugs in ulcerative colitis: insights from machine learning and molecular docking.. BMC pharmacology & toxicology, 2025. PMID 40361222. DOI 10.1186/s40360-025-00939-7. - Publication context: An integrated machine learning framework for developing and validating diagnostic models and drug predictions based on ulcerative colitis genes.. Frontiers in medicine, 2025. PMID 40584713. DOI 10.3389/fmed.2025.1571529. - 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: ulcerative colitis 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: 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: ### GSE90607 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: Crohn's disease, Fibrosis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 29672662. - Publication context: Fibrostenotic Phenotype of Myofibroblasts in Crohn's Disease is Dependent on Tissue Stiffness and Reversed by LOX Inhibition.. Journal of Crohn's & colitis, 2018. PMID 29672662. DOI 10.1093/ecco-jcc/jjy036. - 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: Crohn's disease 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. - 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: ### GSE92415 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: Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 21 publications; 21 DOIs available: PMID 23735746, PMID 34306038, PMID 37322958, PMID 38026254, PMID 38352118. - Publication context: Subcutaneous golimumab induces clinical response and remission in patients with moderate-to-severe ulcerative colitis.. Gastroenterology, 2014. PMID 23735746. DOI 10.1053/j.gastro.2013.05.048. - Publication context: Integrated Analysis of Multiple Microarray Studies to Identify Novel Gene Signatures in Ulcerative Colitis.. Frontiers in genetics, 2021. PMID 34306038. DOI 10.3389/fgene.2021.697514. - Publication context: Identifying biomarkers associated with the diagnosis of ulcerative colitis via bioinformatics and machine learning.. Mathematical biosciences and engineering : MBE, 2023. PMID 37322958. DOI 10.3934/mbe.2023476. - 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: treated 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: 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 treatment/control experiment. - 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: ### GSE9452 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: Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 5 publications; 5 DOIs available: PMID 19177426, PMID 29794741, PMID 33132321, PMID 35497913, PMID 37078344. - Publication context: Diagnosis of ulcerative colitis before onset of inflammation by multivariate modeling of genome-wide gene expression data.. Inflammatory bowel diseases, 2009. PMID 19177426. DOI 10.1002/ibd.20879. - Publication context: Identification and analysis of key genes associated with ulcerative colitis based on DNA microarray data.. Medicine, 2018. PMID 29794741. DOI 10.1097/MD.0000000000010658. - Publication context: Bioinformatics Analysis of Key Candidate Genes and Pathways in Ulcerative Colitis.. Biological & pharmaceutical bulletin, 2020. PMID 33132321. DOI 10.1248/bpb.b20-00488. - 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: Inflamed and non-inflamed sample groups detected. - 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: 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: ### GSE94648 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: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 13 publications; 13 DOIs available: PMID 28981629, PMID 34510961, PMID 37055577, PMID 37215183, PMID 37529244. - Publication context: Usefulness of Transcriptional Blood Biomarkers as a Non-invasive Surrogate Marker of Mucosal Healing and Endoscopic Response in Ulcerative Colitis.. Journal of Crohn's & colitis, 2017. PMID 28981629. DOI 10.1093/ecco-jcc/jjx091. - Publication context: Integrative analysis of ferroptosis-related genes in ulcerative colitis.. The Journal of international medical research, 2021. PMID 34510961. DOI 10.1177/03000605211042975. - Publication context: Identification of diagnostic biomarks and immune cell infiltration in ulcerative colitis.. Scientific reports, 2023. PMID 37055577. DOI 10.1038/s41598-023-33388-5. - 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: Case and control sample groups detected: ulcerative colitis 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: 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: 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: ### GSE95095 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: Crohn's disease, Inflammatory bowel disease. - Processed data is available for downstream review. - External evidence: PubMed links 10 publications; 10 DOIs available: PMID 35795659, PMID 36248794, PMID 36714107, PMID 36792688, PMID 37169818. - Publication context: Neutrophil Infiltration Characterized by Upregulation of S100A8, S100A9, S100A12 and CXCR2 Is Associated With the Co-Occurrence of Crohn's Disease and Peripheral Artery Disease.. Frontiers in immunology, 2022. PMID 35795659. DOI 10.3389/fimmu.2022.896645. - Publication context: Identification and validation of the common pathogenesis and hub biomarkers in Hirschsprung disease complicated with Crohn's disease.. Frontiers in immunology, 2022. PMID 36248794. DOI 10.3389/fimmu.2022.961217. - Publication context: Analysis of ferroptosis-associated genes in Crohn's disease based on bioinformatics.. Frontiers in medicine, 2022. PMID 36714107. DOI 10.3389/fmed.2022.1058076. - Publication context: 7 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: Crohn's disease 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: 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 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: ### GSE96665 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: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 28806280, PMID 35705632. - Publication context: Integrated Analysis of Biopsies from Inflammatory Bowel Disease Patients Identifies SAA1 as a Link Between Mucosal Microbes with TH17 and TH22 Cells.. Inflammatory bowel diseases, 2017. PMID 28806280. DOI 10.1097/MIB.0000000000001208. - Publication context: Identification of useful genes from multiple microarrays for ulcerative colitis diagnosis based on machine learning methods.. Scientific reports, 2022. PMID 35705632. DOI 10.1038/s41598-022-14048-6. - 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: inflamed tissue 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. - 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: 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: ### GSE100922 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. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 30521002. - Publication context: Differences in Peripheral and Tissue Immune Cell Populations Following Haematopoietic Stem Cell Transplantation in Crohn's Disease Patients.. Journal of Crohn's & colitis, 2019. PMID 30521002. DOI 10.1093/ecco-jcc/jjy203. - 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: 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: ### GSE101816 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: Crohn's disease, Inflammatory bowel disease. - Processed data is available for downstream review. - External evidence: PubMed links 3 publications; 3 DOIs available: PMID 30282822, PMID 32561494, PMID 38385744. - Publication context: Colonic epithelial miR-31 associates with the development of Crohn's phenotypes.. JCI insight, 2018. PMID 30282822. DOI 10.1172/jci.insight.122788. - Publication context: Decreased Colonic Activin Receptor-Like Kinase 1 Disrupts Epithelial Barrier Integrity in Patients With Crohn's Disease.. Cellular and molecular gastroenterology and hepatology, 2020. PMID 32561494. DOI 10.1016/j.jcmgh.2020.06.005. - Publication context: Aberrant miR-29 is a predictive feature of severe phenotypes in pediatric Crohn's disease.. JCI insight, 2024. PMID 38385744. DOI 10.1172/jci.insight.168800. - 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: 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 secondary RNA assays are not primary mRNA tissue RNA-seq. - DOWNGRADE_REASON: Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq. - 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: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. - 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: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE101817 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: Crohn's disease, Inflammatory bowel disease. - Processed data is available for downstream review. - External evidence: PubMed links 3 publications; 3 DOIs available: PMID 30282822, PMID 32561494, PMID 38385744. - Publication context: Colonic epithelial miR-31 associates with the development of Crohn's phenotypes.. JCI insight, 2018. PMID 30282822. DOI 10.1172/jci.insight.122788. - Publication context: Decreased Colonic Activin Receptor-Like Kinase 1 Disrupts Epithelial Barrier Integrity in Patients With Crohn's Disease.. Cellular and molecular gastroenterology and hepatology, 2020. PMID 32561494. DOI 10.1016/j.jcmgh.2020.06.005. - Publication context: Aberrant miR-29 is a predictive feature of severe phenotypes in pediatric Crohn's disease.. JCI insight, 2024. PMID 38385744. DOI 10.1172/jci.insight.168800. - 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: 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 secondary RNA assays are not primary mRNA tissue RNA-seq. - DOWNGRADE_REASON: Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq. - 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: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. - 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: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE107865 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, Inflammatory bowel disease. - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 29618496, PMID 32104045. - Publication context: Cell-centred meta-analysis reveals baseline predictors of anti-TNFα non-response in biopsy and blood of patients with IBD.. Gut, 2019. PMID 29618496. DOI 10.1136/gutjnl-2017-315494. - 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. - 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: 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. - 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: - 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: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE122618 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: Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 30329026. - Publication context: ANP32E, a Protein Involved in Steroid-Refractoriness in Ulcerative Colitis, Identified by a Systems Biology Approach.. Journal of Crohn's & colitis, 2019. PMID 30329026. DOI 10.1093/ecco-jcc/jjy171. - 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: 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 secondary RNA assays are not primary mRNA tissue RNA-seq. - DOWNGRADE_REASON: Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq. - 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: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. - 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: - SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; 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: ### GSE130038 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: Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 31826065. - Publication context: Elevated Colonic Mucin Expression Correlates with Extended Time to Surgery for Ulcerative Colitis Patients.. Journal of gastrointestinal and liver diseases : JGLD, 2019. PMID 31826065. DOI 10.15403/jgld-250. - 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: 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: ### GSE150961 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: Ulcerative colitis. - 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. - 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: 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: ### GSE156044 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: Crohn's disease, Fibrosis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 32991841. - Publication context: Translocation of Viable Gut Microbiota to Mesenteric Adipose Drives Formation of Creeping Fat in Humans.. Cell, 2020. PMID 32991841. DOI 10.1016/j.cell.2020.09.009. - 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: 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: ### GSE156453 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: Colorectal cancer, Crohn's disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 33384384. - Publication context: In Vivo Gene Expression Profile of Human Intestinal Epithelial Cells: From the Viewpoint of Drug Metabolism and Pharmacokinetics.. Drug metabolism and disposition: the biological fate of chemicals, 2021. PMID 33384384. DOI 10.1124/dmd.120.000283. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Excluded sample type flags reduce suitability. - DOWNGRADE_REASON: Excluded sample type flags reduce suitability. - 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: 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: 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_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: 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_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: GSM4731853, GSM4731854, GSM4731855, GSM4731856, GSM4731857, GSM4731858, GSM4731862 - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE157020 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: Crohn's disease. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 36521659. - Publication context: Dysfunctional Extracellular Matrix Remodeling Supports Perianal Fistulizing Crohn's Disease by a Mechanoregulated Activation of the Epithelial-to-Mesenchymal Transition.. Cellular and molecular gastroenterology and hepatology, 2023. PMID 36521659. DOI 10.1016/j.jcmgh.2022.12.006. - 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: ### GSE15933 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: Crohn's disease, Fibrosis, Inflammatory bowel disease, Ulcerative colitis. - 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: 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: 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. - 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: ### GSE186963 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, Inflammatory bowel disease, 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: 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: 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: ### GSE212849 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: Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 36170836. - Publication context: Cytokine responsive networks in human colonic epithelial organoids unveil a molecular classification of inflammatory bowel disease.. Cell reports, 2022. PMID 36170836. DOI 10.1016/j.celrep.2022.111439. - 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: ### GSE215285 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: Inflammatory bowel disease. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 37132462. - Publication context: Regional Transcriptomics and Proteomics of Pharmacokinetics-Related Genes in Human Intestine.. Molecular pharmaceutics, 2023. PMID 37132462. DOI 10.1021/acs.molpharmaceut.2c01002. - 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: ### GSE217352 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. - Prioritized assay: bulk RNA-seq is the active assay expectation. - Interpreted disease metadata: Crohn's disease, Inflammatory bowel disease. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 41821786. - Publication context: A blood-based transcriptomic signature stratifies severe Crohn's disease and defines potentially targetable therapeutic pathways.. Frontiers in gastroenterology (Lausanne, Switzerland), 2023. PMID 41821786. DOI 10.3389/fgstr.2023.1251133. - 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. - 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: 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. - 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. - 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: - 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: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE228122 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: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 37736163. - Publication context: Patient-derived Colonoids From Disease-spared Tissue Retain Inflammatory Bowel Disease-specific Transcriptomic Signatures.. Gastro hep advances, 2023. PMID 37736163. DOI 10.1016/j.gastha.2023.05.003. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Excluded sample type flags reduce suitability. - DOWNGRADE_REASON: Excluded sample type flags reduce suitability. - 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: 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: 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_SAMPLE_TYPES [warning]: Multiple sample type labels or exclusion flags were detected. - WARNING_CODE: ORGANOIDS_INCLUDED [warning]: Organoid samples appear to be included. - WARNING_CODE: AMBIGUOUS_SAMPLES_DETECTED [info]: Ambiguous sample metadata was detected in 1 sample(s): GSM7114773 matched "disease state: NA". Review these samples before inclusion or manual group assignment. - 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_SAMPLE_TYPES [WARNING]: Multiple sample type labels or exclusion flags were detected.; samples: - ORGANOIDS_INCLUDED [WARNING]: Organoid samples appear to be included.; samples: GSM7114764, GSM7114765, GSM7114766, GSM7114767, GSM7114768, GSM7114769, GSM7114770, GSM7114771, GSM7114772, GSM7114773, GSM7114774, GSM7114775, GSM7114776, GSM7114777, GSM7114778, GSM7114779, GSM7114780, GSM7114781, GSM7114782, GSM7114783, GSM7114784, GSM7114785, GSM7114786, GSM7114787, GSM7114788, GSM7114789, GSM7114790, GSM7114791, GSM7114792, GSM7114793, GSM7114794, GSM7114795, GSM7114796, GSM7114797, GSM7114798, GSM7114799, GSM7114800, GSM7114801, GSM7114802, GSM7114803, GSM7114804, GSM7114805, GSM7114806, GSM7114807, GSM7114808, GSM7114809, GSM7114810, GSM7114811, GSM7114812, GSM7114813, GSM7114814, GSM7114815, GSM7114816, GSM7114817, GSM7114818, GSM7114819, GSM7114820 - AMBIGUOUS_SAMPLES_DETECTED [INFO]: Ambiguous sample metadata was detected in 1 sample(s): GSM7114773 matched "disease state: NA". Review these samples before inclusion or manual group assignment.; samples: GSM7114773 - 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: ### GSE236055 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: Colorectal cancer, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 40989939. - Publication context: Colonic Mucosal Gene Expression Profile in Patients with Neoplastic Progression in Longstanding Ulcerative Colitis.. Clinical and experimental gastroenterology, 2025. PMID 40989939. DOI 10.2147/CEG.S528854. - 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: ### GSE247146 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: Inflammatory bowel disease. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 38401525. - Publication context: Blood gene expression biomarkers of response to anti-TNF drugs in pediatric inflammatory bowel diseases before initiation of treatment.. Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie, 2024. PMID 38401525. DOI 10.1016/j.biopha.2024.116299. - 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: 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: ### GSE25220 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: Colorectal cancer, Inflammatory bowel disease. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 21669488. - Publication context: N-nitroso compound exposure-associated transcriptomic profiles are indicative of an increased risk for colorectal cancer.. Cancer letters, 2011. PMID 21669488. DOI 10.1016/j.canlet.2011.05.007. - 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: ### GSE25275 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: Infectious disease or host response, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 21123809. - Publication context: IL-22+ CD4+ T cells are associated with therapeutic trichuris trichiura infection in an ulcerative colitis patient.. Science translational medicine, 2010. PMID 21123809. DOI 10.1126/scitranslmed.3001500. - 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: 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: ### GSE25276 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: Infectious disease or host response, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 21123809. - Publication context: IL-22+ CD4+ T cells are associated with therapeutic trichuris trichiura infection in an ulcerative colitis patient.. Science translational medicine, 2010. PMID 21123809. DOI 10.1126/scitranslmed.3001500. - 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: 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: ### GSE25277 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: Infectious disease or host response, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 21123809. - Publication context: IL-22+ CD4+ T cells are associated with therapeutic trichuris trichiura infection in an ulcerative colitis patient.. Science translational medicine, 2010. PMID 21123809. DOI 10.1126/scitranslmed.3001500. - 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: 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: ### GSE268273 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: Fibrosis, Inflammatory bowel disease, Liver fibrosis, Metabolic disease, Steatohepatitis (NASH/MASH), Steatotic liver disease (NAFLD/MASLD), Type 2 diabetes. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 39411649. - Publication context: Clinical and molecular characterization of steatotic liver disease in the setting of immune-mediated inflammatory diseases.. JHEP reports : innovation in hepatology, 2024. PMID 39411649. DOI 10.1016/j.jhepr.2024.101167. - 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: ### GSE276395 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, Inflammatory bowel disease. - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 39684365, PMID 39894009. - Publication context: Gene Expression Dysregulation in Whole Blood of Patients with Clostridioides difficile Infection.. International journal of molecular sciences, 2024. PMID 39684365. DOI 10.3390/ijms252312653. - Publication context: Blood transcriptomics identifies FEZ1 as a potential biomarker for inflammatory bowel disease.. Computers in biology and medicine, 2025. PMID 39894009. DOI 10.1016/j.compbiomed.2025.109742. - 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: 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: ### GSE279302 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: Inflammatory bowel disease. - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 39464142, PMID 41688467. - Publication context: eQTL in diseased colon tissue identifies novel target genes associated with IBD.. bioRxiv : the preprint server for biology, 2024. PMID 39464142. DOI 10.1101/2024.10.14.618229. - Publication context: eQTL in diseased colon tissue identifies potential target genes associated with IBD.. Nature communications, 2026. PMID 41688467. DOI 10.1038/s41467-026-69364-6. - 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. - 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: 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: ### GSE317503 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: Crohn's disease, Inflammatory bowel disease. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 42185506. - Publication context: Reference-guided genome assembly of long non-coding rna transcripts reveals target genes associated with Crohn's disease.. Scientific reports, 2026. PMID 42185506. DOI 10.1038/s41598-026-54788-3. - 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: 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: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. - 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. - SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; 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: ### GSE33078 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Cell line. 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: Crohn's disease. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 22760007. - Publication context: Identification of a potential physiological precursor of aberrant cells in refractory coeliac disease type II.. Gut, 2013. PMID 22760007. DOI 10.1136/gutjnl-2012-302265. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Excluded sample type flags reduce suitability. - DOWNGRADE_REASON: Excluded sample type flags reduce suitability. - 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: 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: 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: Cell line. 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: 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: 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: - 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: GSM819181, GSM819182, GSM819183, GSM819184, GSM819185, GSM819186, GSM819187, GSM819188, GSM819189, GSM819190, GSM819191, GSM819192, GSM819193, GSM819194, GSM819195, GSM819196, GSM819197, GSM819198, GSM819199, GSM819200, GSM819201, GSM819202 - 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: ### GSE46754 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: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 24205244. - Publication context: Differences in visceral fat and fat bacterial colonization between ulcerative colitis and Crohn's disease. An in vivo and in vitro study.. PloS one, 2013. PMID 24205244. DOI 10.1371/journal.pone.0078495. - 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: ### GSE69762 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: Crohn's disease, Inflammatory bowel disease. - 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 26891258, PMID 39159791. - Publication context: Reduced Human α-defensin 6 in Noninflamed Jejunal Tissue of Patients with Crohn's Disease.. Inflammatory bowel diseases, 2016. PMID 26891258. DOI 10.1097/MIB.0000000000000707. - Publication context: Identifying the importance of PCK1 in maintaining ileal epithelial barrier integrity in Crohn's disease.. Gene, 2024. PMID 39159791. DOI 10.1016/j.gene.2024.148872. - 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. - DOWNGRADE_REASON: Publication context: Reduced Human α-defensin 6 in Noninflamed Jejunal Tissue of Patients with Crohn's Disease.. Inflammatory bowel diseases, 2016. PMID 26891258. DOI 10.1097/MIB.0000000000000707. - 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: ### GSE74265 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: Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 28652445, PMID 35705632. - Publication context: Increased Copy Number Variation of mtDNA in an Array-based Digital PCR Assay Predicts Ulcerative Colitis-associated Colorectal Cancer.. In vivo (Athens, Greece), 2017. PMID 28652445. DOI 10.21873/invivo.11119. - Publication context: Identification of useful genes from multiple microarrays for ulcerative colitis diagnosis based on machine learning methods.. Scientific reports, 2022. PMID 35705632. DOI 10.1038/s41598-022-14048-6. - 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: ### GSE77013 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: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 27492330. - Publication context: A long noncoding RNA signature for ulcerative colitis identifies IFNG-AS1 as an enhancer of inflammation.. American journal of physiology. Gastrointestinal and liver physiology, 2016. PMID 27492330. DOI 10.1152/ajpgi.00212.2016. - 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: 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: ### GSE87465 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: Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 29401083. - Publication context: Molecular Comparison of Adult and Pediatric Ulcerative Colitis Indicates Broad Similarity of Molecular Pathways in Disease Tissue.. Journal of pediatric gastroenterology and nutrition, 2018. PMID 29401083. DOI 10.1097/MPG.0000000000001898. - 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: ### GSE102524 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: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis. - Processed data is available for downstream review. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: cancer 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: 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. - 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: ### GSE230539 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: Inflammatory bowel disease. - Processed data is available for downstream review. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: inflammatory bowel disease 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. - 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. - 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: 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: ### GSE23552 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: Asthma, Inflammatory bowel disease. - Processed data is available for downstream review. - External evidence: PubMed links 6 publications; 5 DOIs available: PMID 20625511, PMID 33603773, PMID 36059464, PMID 36915741, PMID 39986126. - Publication context: Gene transcription changes in asthmatic chronic rhinosinusitis with nasal polyps and comparison to those in atopic dermatitis.. PloS one, 2010. PMID 20625511. DOI 10.1371/journal.pone.0011450. - Publication context: Transcriptomic Signatures and Functional Network Analysis of Chronic Rhinosinusitis With Nasal Polyps.. Frontiers in genetics, 2021. PMID 33603773. DOI 10.3389/fgene.2021.609754. - Publication context: Identification of key genes and pathways in chronic rhinosinusitis with nasal polyps and asthma comorbidity using bioinformatics approaches.. Frontiers in immunology, 2022. PMID 36059464. DOI 10.3389/fimmu.2022.941547. - Publication context: 3 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: allergic rhinitis 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: 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. - 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: ### GSE69446 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: Crohn's disease. - 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 29263823. - Publication context: Relation between NOD2 genotype and changes in innate signaling in Crohn's disease on mRNA and miRNA levels.. NPJ genomic medicine, 2017. PMID 29263823. DOI 10.1038/s41525-016-0001-4. - 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: 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. - 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: 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 secondary RNA assays are not primary mRNA tissue RNA-seq. - DOWNGRADE_REASON: Overall score capped because secondary RNA assays are not primary mRNA tissue RNA-seq. - 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: 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: SECONDARY_ASSAY_CONTEXT [warning]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. - 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. - TREATED_SAMPLES_NEED_REVIEW [INFO]: Treated samples may need review depending on the comparison.; samples: GSM1701327, GSM1701328, GSM1701329, GSM1701333, GSM1701334, GSM1701337, GSM1701338, GSM1701341, GSM1701342, GSM1701343, GSM1701347, GSM1701348, GSM1701351, GSM1701352 - TREATED_AND_UNTREATED_SAMPLES_MIXED [INFO]: Treated and untreated samples are both present.; samples: - SECONDARY_ASSAY_CONTEXT [WARNING]: Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.; 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: ### GSE148233 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: Crohn's disease, Ulcerative colitis. - 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. - 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: 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: - 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: ### GSE150979 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: Melanoma, Ulcerative colitis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 33707310. - Publication context: Pro- and Antitumorigenic Capacity of Immunoproteasomes in Shaping the Tumor Microenvironment.. Cancer immunology research, 2021. PMID 33707310. DOI 10.1158/2326-6066.CIR-20-0492. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Control type metadata 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: 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: 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: 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: 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. - 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: - 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: ### GSE20941 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: Crohn's disease. - 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: 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 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: ### GSE60083 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: Crohn's disease. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 24943399. - Publication context: Disruption of macrophage pro-inflammatory cytokine release in Crohn's disease is associated with reduced optineurin expression in a subset of patients.. Immunology, 2015. PMID 24943399. DOI 10.1111/imm.12338. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Control type metadata 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. - 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: 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: 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. - DOWNGRADE_REASON: Publication context: Disruption of macrophage pro-inflammatory cytokine release in Crohn's disease is associated with reduced optineurin expression in a subset of patients.. Immunology, 2015. PMID 24943399. DOI 10.1111/imm.12338. - 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. - 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: