Ranked GEO Datasets

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Explore premium collections with reusable study, cohort and sample curation. The matching scope is stated for each collection. Organism, tissue, comparison and sample requirements still need review; collection availability does not affect dataset ranking.

Liver Fibrosis Expression Collection

Disease scope matches your disease term.

Public liver fibrosis expression datasets with disease stage or fibrosis/control comparisons.

Preview fixture · Version v0.1-preview

Study inventory: 3 datasets
Reported sample inventory: 316 samples
Updated: 2026-06-22
Disease: Liver fibrosis
Organisms: Homo sapiens, Mus musculus
Technologies: bulk RNA-seq, microarray
Tissues: liver tissue, liver biopsy
Comparisons: fibrosis vs control, advanced fibrosis vs mild fibrosis, disease model vs control

Query overlap with this collection version
Dimension	Your query	Collection scope	Comparison
Disease	Liver fibrosis	Liver fibrosis	MATCH Declared collection scope includes this requested dimension; question-specific sample eligibility still needs review.
Specimen		liver tissue, liver biopsy	NOT_REQUESTED No explicit query requirement was supplied for this dimension.
Organism		Homo sapiens, Mus musculus	NOT_REQUESTED No explicit query requirement was supplied for this dimension.
Comparison		fibrosis vs control, advanced fibrosis vs mild fibrosis, disease model vs control	NOT_REQUESTED No explicit query requirement was supplied for this dimension.

Full access adds reusable curated cohort structure, sample decisions and provenance. Review the content status above before treating a release as professionally approved. Ordinary Search results remain available below.

Preview collection

Counts describe the collection inventory, not final eligible samples or independent subjects. Preview fixtures are illustrative; review-pending releases are not professionally approved.

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15 shown of 17 matching datasets Comparison Tumor vs normal Tissue/sample context Patient tissue Organism Any organism Assay Any assay Ranking defaults Modified 6 user changes 1 active filters Page 1 of 2 · showing 1-15

Disease/condition e.g. colorectal cancer Anatomical source Specimen material Cell population Comparison type (required) Organism Assay type Minimum samples Experimental model Exclude cell lines Require processed data GEO only recount3 available Expression Atlas available

Treatment requirements Optional See what each comparison arm must satisfy — Unrestricted

Comparison: Tumor vs normal

Case arm

Your requirement

Exposure state

Agent

Comparator

From comparison

Determined by comparison

For treatment vs control, use a named agent, an explicit collection window and an exposed or unexposed state. The comparator needs the opposite reported exposure state for the same agent, target and window.

Collection window Assertion target

Named agent if supplied; otherwise all interventions.

Scope & matching · additional options

Exposure scopeAutomatic: named agent if supplied; otherwise all interventions. Uncertain alternativesReview cases are not confirmed matches. Exact reported scope (when requested)

Missing metadata never proves no exposure.

Evidence and comparison rules

Exact results require an eligible sample subset and reported independent subjects in both arms.

“No exposure” applies only to the selected agent, target and time window. No exposure to a new agent before collection does not rule out earlier therapy.

A broader treatment history requires separate, explicit evidence and may be unavailable. All prior therapy requires a through-collection window.

Planned exposure does not establish that treatment occurred. Treatment vs control requires an exposed or unexposed state, a named agent and an explicit collection window.

Organism and specimen requirements apply to both arms. For treatment vs control, disease requirements also apply to both arms.

Genotype requirements Optional Define a requirement, then assign it to samples — Unrestricted

Genetic state Gene symbol

Apply requirement to

Specific protein variant · optional

Exact reported protein variant

Leave blank for a gene-level requirement. A variant restriction applies to every selected arm.

Genotype describes sampled material. Confirmed evidence must come from the same samples as your other requirements.

Use with human bulk RNA-seq or expression microarray.

Evidence and comparison rules

Select Homo sapiens and a supported assay in the search filters.

Missing genotype does not establish wild type. Both comparison arms still need eligible, independent samples.

A subject's carrier status does not establish the sampled tumor's genotype or disease.

Clear filters Ranking defaults Relax defaults

Showing one page of matching results. Use next/previous for browsing, or CSV/Markdown export for the full matching set.

Strict results

These datasets meet every active search criterion.

Aanalysis transcriptomes of Schisandrin B alleviates CCl4-induced liver fibrosis in rats by RNA-sequencing

Select

Organization: Third Affiliated Hospital of Second Military Medical University

Case treated Control normal tissue

Treatment vs control Tissue

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

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.

info Treated samples may need review depending on the comparison. critical Dataset organism does not match the human patient-tissue tumor-normal intent.

Influence of Liver Fibrosis on Pien Tze Huang by RNA-Seq Analysis of Circular RNAs

Select

Organization: Shanghai Jiao Tong University

Case treated Control control

Treatment vs control Tissue

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

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.

warning Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. critical Dataset organism does not match the human patient-tissue tumor-normal intent.

The next-generation sequencing was helpful for the quantitative analysis of the normal control group and the liver fibrosis group

Select

Organization: Cichunwu

Case liver fibrosis Control healthy control

Disease/model vs control Tissue

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

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.

No warnings

Development of gene expression signatures for human liver fibrosis

Select

Organization: Shanghai University of traditional Chinese Medicine

Case liver fibrosis Control healthy control

Disease/model vs control Biopsy

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

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.

warning Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. info Microarray expression context was detected; compare separately from RNA-seq cohorts. warning Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.

Resident Kupffer cell maladaptation in Liver Fibrosis is Rescued by Monocyte-Derived Syncytia of Macrophages

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Organization: University of Calgary

Case treated Control untreated

Treatment vs control Tissue

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

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.

critical Dataset organism does not match the human patient-tissue tumor-normal intent.

Mild vs advanced liver fibrosis

Select

Organization: Faculty of Medicine and Pharmacy

Case liver fibrosis Control unclear

Unclear study design Tissue

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

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.

critical No clear control group was detected from normalized metadata. info Microarray expression context was detected; compare separately from RNA-seq cohorts. warning Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. warning Patient-tissue tumor-normal intent requires clear tumor-normal grouping.

miR-579-3p controls hepatocellular carcinoma formation by regulating the PI3K-AKT pathway in chronically inflamed liver (mRNA expression)

Select

Organization: University of Basel

Case liver fibrosis Control unclear

Unclear study design Biopsy

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

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.

critical No clear control group was detected from normalized metadata. warning Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. info Microarray expression context was detected; compare separately from RNA-seq cohorts. warning Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. warning Patient-tissue tumor-normal intent requires clear tumor-normal grouping.

Expression data for participants in iWITH study at screening visit

Select

Organization: Immune Tolerance Network

Case inflamed tissue Control unclear

Unclear study design Biopsy

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

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.

Identification of miRNAs as biomarkers of drug response of Pien Tze Huang in Hepatic Fibrosis Treatments

Select

Organization: Shanghai Jiao Tong University

Case liver fibrosis Control unclear

Unclear study design Tissue

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

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.

critical No clear control group was detected from normalized metadata. warning Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. critical Dataset organism does not match the human patient-tissue tumor-normal intent. warning Patient-tissue tumor-normal intent requires clear tumor-normal grouping.

Prognostic Liver Signature profiles in biopsy tissues from non-alcoholic fatty liver disease (NAFLD) patients in the U.S.

Select

Organization: University of Texas Southwestern Medical Center

Case liver fibrosis Control unclear

Unclear study design Unclear specimen/source

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

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.

Transcriptome profile of liver biopsy tissues from patients with non-alcoholic fatty liver disease (derivation set).

Select

Organization: Mie University

Case liver fibrosis Control unclear

Unclear study design Tissue

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

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.

critical No clear control group was detected from normalized metadata. warning Patient-tissue tumor-normal intent requires clear tumor-normal grouping.

Transcriptome profile of liver biopsy tissues from patients with non-alcoholic fatty liver disease (tissue validation set 1).

Select

Organization: University of Texas Southwestern Medical Center

Case liver fibrosis Control unclear

Unclear study design Biopsy

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

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.

critical No clear control group was detected from normalized metadata. warning Patient-tissue tumor-normal intent requires clear tumor-normal grouping.

Transcriptome profile of liver biopsy tissues from patients with non-alcoholic fatty liver disease (tissue validation set 2).

Select

Organization: University of Texas Southwestern Medical Center

Case liver fibrosis Control unclear

Unclear study design Tissue

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

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.

critical No clear control group was detected from normalized metadata. warning Patient-tissue tumor-normal intent requires clear tumor-normal grouping.

Gene expression profiling in HCV associated liver disease

Select

Organization: University of the Punjab

Case liver fibrosis Control unclear

Unclear study design Biopsy

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

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.

Expression data for Nonalcoholic fatty liver disease patients

Select

Organization: Duke University Medical Center

Case liver fibrosis Control unclear

Unclear study design Biopsy

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

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.