# 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:** 2026-10-27T11:44:45.510939660Z - **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: Liver fibrosis - **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=Liver fibrosis; 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: Liver fibrosis - **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: Liver fibrosis - **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 | [GSE110096](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110096) | Aanalysis transcriptomes of Schisandrin B alleviates CCl4-induced liver fibrosis in rats by RNA-sequencing | none | Treatment vs control | Tissue | suitability 0; metadata 100; overall 34 | TREATED_SAMPLES_NEED_REVIEW [info]: Treated samples may need review depending on the comparison.; 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=GSE110096) | Not suitable | | 2 | [GSE150883](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE150883) | Influence of Liver Fibrosis on Pien Tze Huang by RNA-Seq Analysis of Circular RNAs | none | Treatment 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.; 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=GSE150883) | Not suitable | | 3 | [GSE171294](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE171294) | The next-generation sequencing was helpful for the quantitative analysis of the normal control group and the liver fibrosis group | 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=GSE171294) | Not suitable | | 4 | [GSE197112](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE197112) | Development of gene expression signatures for human liver fibrosis | 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=GSE197112) | Not suitable | | 5 | [GSE226946](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE226946) | Resident Kupffer cell maladaptation in Liver Fibrosis is Rescued by Monocyte-Derived Syncytia of Macrophages | 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=GSE226946) | Not suitable | | 6 | [GSE11536](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11536) | Mild vs advanced liver fibrosis | 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=GSE11536) | Not suitable | | 7 | [GSE116044](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE116044) | miR-579-3p controls hepatocellular carcinoma formation by regulating the PI3K-AKT pathway in chronically inflamed liver (mRNA 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.; 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=GSE116044) | Not suitable | | 8 | [GSE118587](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE118587) | Expression data for participants in iWITH study at screening visit | 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=GSE118587) | Not suitable | | 9 | [GSE137100](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE137100) | Identification of miRNAs as biomarkers of drug response of Pien Tze Huang in Hepatic Fibrosis Treatments | 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.; INTENT_ASSAY_MISMATCH [critical]: Dataset organism does not match the human patient-tissue tumor-normal intent.; 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=GSE137100) | Not suitable | | 10 | [GSE150734](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE150734) | Prognostic Liver Signature profiles in biopsy tissues from non-alcoholic fatty liver disease (NAFLD) patients in the U.S. | none | Unclear study design | Unclear specimen/source | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE150734) | Not suitable | | 11 | [GSE192959](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE192959) | Transcriptome profile of liver biopsy tissues from patients with non-alcoholic fatty liver disease (derivation set). | 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=GSE192959) | Not suitable | | 12 | [GSE193066](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE193066) | Transcriptome profile of liver biopsy tissues from patients with non-alcoholic fatty liver disease (tissue validation set 1). | 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=GSE193066) | Not suitable | | 13 | [GSE193080](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE193080) | Transcriptome profile of liver biopsy tissues from patients with non-alcoholic fatty liver disease (tissue validation set 2). | 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=GSE193080) | Not suitable | | 14 | [GSE33258](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE33258) | Gene expression profiling in HCV associated liver disease | 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=GSE33258) | Not suitable | | 15 | [GSE49541](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE49541) | Expression data for Nonalcoholic fatty liver disease patients | 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=GSE49541) | Not suitable | | 16 | [GSE73634](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73634) | Treatment of advanced liver fibrosis in HIV- and HCV-infected adults with simtuzumab, a monoclonal antibody against lysyl oxidase-like 2: Results of a 6-month open-label safety trial | none | Unclear study design | Mixed specimen/source | suitability 0; metadata 93; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. | [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73634) | Not suitable | | 17 | [GSE7741](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7741) | Expression data of HCV-associated advance disease state | none | Unclear study design | Biopsy | suitability 0; metadata 75; overall 34 | NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata.; POOLED_SAMPLES_DETECTED [warning]: Pooled samples were detected and may need exclusion.; 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.; MIXED_DISEASE_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=GSE7741) | Not suitable | ## Ranking explanations ### GSE110096 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: Fibrosis, Liver fibrosis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 42080703. - Publication context: Mechanical stiffness orchestrates distinct regulation of MRTFs and YAP/TAZ transcriptional cofactors in hepatocytes.. The FEBS journal, 2026. PMID 42080703. DOI 10.1111/febs.70570. - 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 normal tissue. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - DOWNGRADE_REASON: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Rule-based grouping found both case and control samples. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: Treatment status metadata normalized where treatment is part of the comparison. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - OVERALL: Overall score capped because 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. - 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: INTENT_ASSAY_MISMATCH [critical]: Dataset organism does not match the human patient-tissue tumor-normal intent. - TREATED_SAMPLES_NEED_REVIEW [INFO]: Treated samples may need review depending on the comparison.; samples: GSM2977565, GSM2977566, GSM2977567 - INTENT_ASSAY_MISMATCH [CRITICAL]: Dataset organism does not match the human patient-tissue tumor-normal intent.; samples: ### GSE150883 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: Fibrosis, Liver fibrosis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 36004475. - Publication context: Identification of circular RNA biomarkers for Pien Tze Huang treatment of CCl4‑induced liver fibrosis using RNA‑sequencing.. Molecular medicine reports, 2022. PMID 36004475. DOI 10.3892/mmr.2022.12825. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Case and control sample groups detected: treated vs control. - COMPARISON_SUITABILITY: 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: 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 treatment/control experiment. - 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: ### GSE171294 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: Fibrosis, Liver cancer, Liver fibrosis. - Processed data is available for downstream review. - External evidence: PubMed links 4 publications; 4 DOIs available: PMID 34336890, PMID 36111046, PMID 36748376, PMID 41651076. - Publication context: Hepatic BRD4 Is Upregulated in Liver Fibrosis of Various Etiologies and Positively Correlated to Fibrotic Severity.. Frontiers in medicine, 2021. PMID 34336890. DOI 10.3389/fmed.2021.683506. - Publication context: Exploration of new therapeutic targets for viral hepatic fibrosis, alcoholic hepatic fibrosis, and non-alcoholic hepatic fibrosis.. Annals of translational medicine, 2022. PMID 36111046. DOI 10.21037/atm-22-3593. - Publication context: Comparative molecular analysis of oral submucous fibrosis and other organ fibrosis based on weighted gene co-expression network analysis.. Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences, 2022. PMID 36748376. DOI 10.11817/j.issn.1672-7347.2022.220452. - 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: liver fibrosis 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. ### GSE197112 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: Fibrosis, Liver fibrosis. - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 38726780, PMID 39426601. - Publication context: Identifying the Crucial Biomarker of MASH-Related HCC.. Combinatorial chemistry & high throughput screening, 2025. PMID 38726780. DOI 10.2174/0113862073287250240424073108. - Publication context: Biological aging accelerates hepatic fibrosis: Insights from the NHANES 2017-2020 and genome-wide association study analysis.. Annals of hepatology, 2025. PMID 39426601. DOI 10.1016/j.aohep.2024.101579. - 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: liver fibrosis 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 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: 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: ### GSE226946 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: Fibrosis, Liver fibrosis. - Processed data is available for downstream review. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: Treated and untreated sample groups detected. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - DOWNGRADE_REASON: Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons. - 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. - OVERALL: Overall score capped because fewer than ten samples limit cohort confidence. - DOWNGRADE_REASON: Overall score capped because fewer than ten samples limit cohort confidence. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - DOWNGRADE_REASON: Downgraded for tissue search because it is a treatment/control experiment. - 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: ### GSE11536 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: Fibrosis, Infectious disease or host response, Liver fibrosis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 19477948. - Publication context: Novel serum markers of fibrosis progression for the follow-up of hepatitis C virus-infected patients.. The American journal of pathology, 2009. PMID 19477948. DOI 10.2353/ajpath.2009.080850. - 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. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because 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: ### GSE116044 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Biopsy. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Fibrosis, Hepatocellular carcinoma, Liver fibrosis. - 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: 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. - 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: ### GSE118587 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Biopsy. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Fibrosis, Liver fibrosis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 30144432. - Publication context: Evidence of Chronic Allograft Injury in Liver Biopsies From Long-term Pediatric Recipients of Liver Transplants.. Gastroenterology, 2018. PMID 30144432. DOI 10.1053/j.gastro.2018.08.023. - 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: ### GSE137100 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, Liver fibrosis. - 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: 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 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. - 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: 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. - 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_ASSAY_MISMATCH [CRITICAL]: Dataset organism does not match the human patient-tissue tumor-normal intent.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: ### GSE150734 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: Alcoholic liver disease, Fibrosis, Liver fibrosis, Steatohepatitis (NASH/MASH), Steatotic liver disease (NAFLD/MASLD). - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 34951993. - Publication context: Molecular Signature Predictive of Long-Term Liver Fibrosis Progression to Inform Antifibrotic Drug Development.. Gastroenterology, 2022. PMID 34951993. DOI 10.1053/j.gastro.2021.12.250. - 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. - COMPARISON_SUITABILITY: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Unclear specimen/source. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE192959 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: Alcoholic liver disease, Fibrosis, Hepatocellular carcinoma, Liver fibrosis, Steatotic liver disease (NAFLD/MASLD). - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 35731891. - Publication context: Molecular signatures of long-term hepatocellular carcinoma risk in nonalcoholic fatty liver disease.. Science translational medicine, 2022. PMID 35731891. DOI 10.1126/scitranslmed.abo4474. - 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: ### GSE193066 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: Alcoholic liver disease, Fibrosis, Hepatocellular carcinoma, Liver fibrosis, Steatotic liver disease (NAFLD/MASLD). - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 35731891, PMID 39271701. - Publication context: Molecular signatures of long-term hepatocellular carcinoma risk in nonalcoholic fatty liver disease.. Science translational medicine, 2022. PMID 35731891. DOI 10.1126/scitranslmed.abo4474. - Publication context: A FAPα-activated MRI nanoprobe for precise grading diagnosis of clinical liver fibrosis.. Nature communications, 2024. PMID 39271701. DOI 10.1038/s41467-024-52308-3. - 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: 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: ### GSE193080 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: Alcoholic liver disease, Fibrosis, Hepatocellular carcinoma, Liver fibrosis, Steatotic liver disease (NAFLD/MASLD). - Processed data is available for downstream review. - External evidence: PubMed links 4 publications; 4 DOIs available: PMID 35731891, PMID 37621719, PMID 39271701, PMID 41240264. - Publication context: Molecular signatures of long-term hepatocellular carcinoma risk in nonalcoholic fatty liver disease.. Science translational medicine, 2022. PMID 35731891. DOI 10.1126/scitranslmed.abo4474. - Publication context: Disseminative Recurrence Signature for Hepatocellular Carcinoma From Nonalcoholic Fatty Liver Disease.. Gastro hep advances, 2023. PMID 37621719. DOI 10.1016/j.gastha.2023.03.021. - Publication context: A FAPα-activated MRI nanoprobe for precise grading diagnosis of clinical liver fibrosis.. Nature communications, 2024. PMID 39271701. DOI 10.1038/s41467-024-52308-3. - Publication context: 1 additional linked PubMed publications are available. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: Tissue. Comparison suitability: 0%. - DOWNGRADE_REASON: Downgraded for tissue search because study design or specimen source is unclear. - MISSING_METADATA: Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear. - 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: ### GSE33258 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Biopsy. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Fibrosis, Infectious disease or host response, Liver fibrosis. - Processed data is available for downstream review. - External evidence: PubMed links 2 publications; 2 DOIs available: PMID 22397681, PMID 32042870. - Publication context: Gene expression profiling of HCV genotype 3a initial liver fibrosis and cirrhosis patients using microarray.. Journal of translational medicine, 2012. PMID 22397681. DOI 10.1186/1479-5876-10-41. - Publication context: HCV infection causes cirrhosis in human by step-wise regulation of host genes involved in cellular functioning and defense during fibrosis: Identification of bio-markers.. Genes & diseases, 2019. PMID 32042870. DOI 10.1016/j.gendis.2019.04.007. - 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: 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: ### GSE49541 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Biopsy. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Fibrosis, Liver cancer, Liver fibrosis, Steatotic liver disease (NAFLD/MASLD). - Processed data is available for downstream review. - External evidence: Expression Atlas curated experiment link is available. - External evidence: PubMed links 18 publications; 18 DOIs available: PMID 23913408, PMID 23916847, PMID 28796060, PMID 29769552, PMID 34572384. - Publication context: Hepatic gene expression profiles differentiate presymptomatic patients with mild versus severe nonalcoholic fatty liver disease.. Hepatology (Baltimore, Md.), 2014. PMID 23913408. DOI 10.1002/hep.26661. - Publication context: Relationship between methylome and transcriptome in patients with nonalcoholic fatty liver disease.. Gastroenterology, 2013. PMID 23916847. DOI 10.1053/j.gastro.2013.07.047. - Publication context: Candidate genes investigation for severe nonalcoholic fatty liver disease based on bioinformatics analysis.. Medicine, 2017. PMID 28796060. DOI 10.1097/MD.0000000000007743. - Publication context: 15 additional linked PubMed publications are available. - RELEVANCE: Disease or condition metadata normalized. - RELEVANCE: Organism normalized. - RELEVANCE: Assay type normalized. - RELEVANCE: Anatomical source metadata normalized. - COMPARISON_SUITABILITY: No excluded sample type flags detected. - COMPARISON_SUITABILITY: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - DOWNGRADE_REASON: Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - MISSING_METADATA: Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Only one side of the comparison is clearly grouped. - METADATA_QUALITY: Disease clarity: Disease or condition metadata normalized. - METADATA_QUALITY: Tissue clarity: Anatomical source metadata normalized. - METADATA_QUALITY: Treatment clarity: No unclear treatment split detected in the sample metadata. - METADATA_QUALITY: Replicate clarity: No pooled sample or technical replicate flags detected. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - RECOMMENDATION_REASON: Not suitable: Dataset does not meet the current suitability threshold. - MISSING_METADATA: Missing or unclear metadata. Comparison - Unclear study design. Specimen: 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: ### GSE73634 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Mixed specimen/source. Comparison suitability: 0%. - Downgraded for tissue search because specimen/source classes are mixed. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Fibrosis, HIV infection, Infectious disease or host response, Liver fibrosis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 27232579. - Publication context: Simtuzumab treatment of advanced liver fibrosis in HIV and HCV-infected adults: results of a 6-month open-label safety trial.. Liver international : official journal of the International Association for the Study of the Liver, 2016. PMID 27232579. DOI 10.1111/liv.13177. - 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. - DOWNGRADE_REASON: Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - WARNING_CODE: NO_CLEAR_CONTROL_GROUP [critical]: No clear control group was detected from normalized metadata. - WARNING_CODE: MICROARRAY_ASSAY_CONTEXT [info]: Microarray expression context was detected; compare separately from RNA-seq cohorts. - WARNING_CODE: INTENT_ASSAY_MISMATCH [warning]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. - WARNING_CODE: INTENT_STUDY_DESIGN_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping. - WARNING_CODE: INTENT_SPECIMEN_SOURCE_UNCLEAR [warning]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity. - NO_CLEAR_CONTROL_GROUP [CRITICAL]: No clear control group was detected from normalized metadata.; samples: - MICROARRAY_ASSAY_CONTEXT [INFO]: Microarray expression context was detected; compare separately from RNA-seq cohorts.; samples: - INTENT_ASSAY_MISMATCH [WARNING]: Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.; samples: - INTENT_STUDY_DESIGN_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires clear tumor-normal grouping.; samples: - INTENT_SPECIMEN_SOURCE_UNCLEAR [WARNING]: Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.; samples: ### GSE7741 Dataset does not meet the current suitability threshold. - Comparison: Unclear study design. Specimen: Biopsy. Comparison suitability: 0%. - Downgraded for tissue search because study design or specimen source is unclear. - Downgraded assay: microarray cohorts are separated from the RNA-seq intent. - Interpreted disease metadata: Fibrosis, Infectious disease or host response, Liver fibrosis. - Processed data is available for downstream review. - External evidence: PubMed links 1 publication; 1 DOI available: PMID 21484131. - Publication context: Gene profiling of early and advanced liver disease in chronic hepatitis C patients.. Hepatology international, 2011. PMID 21484131. DOI 10.1007/s12072-011-9252-4. - 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. - COMPARISON_SUITABILITY: Pooled or technical replicate samples reduce suitability. - DOWNGRADE_REASON: Pooled or technical replicate samples reduce suitability. - METADATA_QUALITY: Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. - METADATA_QUALITY: Group clarity: Case and control groups are not clear from sample metadata. - MISSING_METADATA: Missing or unclear metadata. Group clarity - Case and control groups are not clear from sample metadata. - 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: Pooled samples or technical replicates need review before trusting group counts. - METADATA_QUALITY: Data availability clarity: Dataset-level processed or raw data availability is explicit. - DATA_AVAILABILITY: Processed data available. - DATA_AVAILABILITY: Raw data available. - OVERALL: Weighted score: 30% metadata coverage, 30% comparison suitability, 25% metadata quality, 15% data availability. - OVERALL: Overall score capped because comparison suitability is weak for the selected search intent. - DOWNGRADE_REASON: Overall score capped because comparison suitability is weak for the selected search intent. - 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: 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: POOLED_SAMPLES_DETECTED [warning]: Pooled samples were detected and may need exclusion. - 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: MIXED_DISEASE_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: - POOLED_SAMPLES_DETECTED [WARNING]: Pooled samples were detected and may need exclusion.; samples: GSM182149, GSM182150, GSM182151 - 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: - MIXED_DISEASE_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: