GSE49541

Expression data for Nonalcoholic fatty liver disease patients

Whole-study status Not suitable

Dataset does not meet the current suitability threshold.

Whole-study downloads — these do not apply your sample requirements.

Selected cohort requirements

Samples meeting selected requirements: 0 cases / 0 controls

View matching samples

72 case / 0 control samples elsewhere in the study have incomplete or conflicting evidence; they are not included above

Patient pairs verified in indexed sample metadata: 0

A case/control comparison meeting these requirements is not confirmed.

Counts describe samples, not independent patients. Pair verification uses explicit subject identifiers in indexed sample metadata. Zero verified pairs does not establish that the study is unpaired; reported matched-normal design alone is insufficient.

Summary

Nonalcoholic fatty liver disease represents a spectrum of pathology that ranges from benign steatosis to potentially-progressive steatohepatitis and affects more than 30% of US adults. Advanced NAFLD is associated with increased morbidity and mortality from cirrhosis, primary liver cancer, cardiovascular disease and extrahepatic cancers. Accurate identification of patients at risk for advanced NAFLD is challenging. The aims of this study were to define the liver gene expression patterns that distinguish mild from advanced NAFLD and to develop a gene expression profile associated with advanced NAFLD.

Overall design

We analyzed total RNA from 72 patients with NAFLD (40 with mild NAFLD, fibrosis stage 0-1 and 32 with advanced NAFLD, fibrosis stage 3-4) and developed a gene profile associated with advanced NAFLD.

Source Evidence

4 sources
Source Contribution Status
GEO

Original dataset metadata, sample metadata, source links, and GEO data availability flags.

Sample records
72 GSM samples
Primary source
recount3

Planned trusted source for processed count availability.

No match found
Expression Atlas

Curated expression experiment linkage and source URL.

Expression Atlas accession
E-GEOD-49541
Available
PubMed

Primary GEO citations and related PubMed articles that mention this dataset.

18 linked publications 18 DOIs

Primary publication

  1. Hepatic gene expression profiles differentiate presymptomatic patients with mild versus severe nonalcoholic fatty liver disease. Hepatology (Baltimore, Md.), 2014
  2. Relationship between methylome and transcriptome in patients with nonalcoholic fatty liver disease. Gastroenterology, 2013

Related publications

  1. (-)-Epicatechin targets early growth response protein 1, an inflammation-associated ferroptosis regulator, to ameliorate metabolic dysfunction-associated steatotic liver disease. Biochemical pharmacology, 2025
  2. Identification of key genes and pathways in mild and severe nonalcoholic fatty liver disease by integrative analysis. Chronic diseases and translational medicine, 2021
  3. A comprehensive bioinformatics analysis on multiple Gene Expression Omnibus datasets of nonalcoholic fatty liver disease and nonalcoholic steatohepatitis. Scientific reports, 2018
  4. Diagnostic role of SPP1 and collagen IV in a rat model of type 2 diabetes mellitus with MASLD. Scientific reports, 2024
  5. PI3K/AKT signaling pathway plays an important role in the pathogenesis of metabolic dysfunction-associated steatotic liver disease. Scientific reports, 2025
  6. Candidate genes investigation for severe nonalcoholic fatty liver disease based on bioinformatics analysis. Medicine, 2017
  7. Neutrophil extracellular trapping network-associated biomarkers in liver fibrosis: machine learning and experimental validation. Journal of translational medicine, 2025
  8. Identifying the Crucial Biomarker of MASH-Related HCC. Combinatorial chemistry & high throughput screening, 2025
  9. Microarray-based Detection of Critical Overexpressed Genes in the Progression of Hepatic Fibrosis in Non-alcoholic Fatty Liver Disease: A Protein-protein Interaction Network Analysis. Current medicinal chemistry, 2024
  10. Identification of common signature genes and pathways underlying the pathogenesis association between nonalcoholic fatty liver disease and atherosclerosis. Frontiers in cardiovascular medicine, 2023
  11. Machine learning and experimental validation identified autophagy signature in hepatic fibrosis. Frontiers in immunology, 2024
  12. Identification of regulatory cell death-related genes during MASH progression using bioinformatics analysis and machine learning strategies. Frontiers in immunology, 2025
  13. Identification of glycolysis-related clusters and immune cell infiltration in hepatic fibrosis progression using machine learning models and experimental validation. Frontiers in immunology, 2025
  14. NUSAP1 Could be a Potential Target for Preventing NAFLD Progression to Liver Cancer. Frontiers in pharmacology, 2022
  15. Modelling Nonalcoholic Steatohepatitis In Vivo-A Close Transcriptomic Similarity Supports the Guinea Pig Disease Model. Biomedicines, 2021
  16. From a Multi-Omics Signature to a Therapeutic Candidate: Computational Prediction and Experimental Validation in Liver Fibrosis. Pharmaceuticals (Basel, Switzerland), 2026
Available

Metadata Quality Components

Analysis Readiness

Not ready
55% DE readiness

Contrast completeness

10/25 pts

Only one side of the contrast is present; downstream DE needs both groups.

Minimum group size

0/20 pts

Minimum group size cannot be evaluated until a complete contrast exists.

Processed data availability

20/20 pts

Processed data is marked available in the GEO index.

Sample decision clarity

15/15 pts

All samples are assigned to a case or control group.

Blocking warnings

0/10 pts

Critical warnings must be resolved before downstream analysis.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

  • No complete case/control contrast is available.
  • Critical dataset warnings must be resolved.

Next Steps

  • Resolve critical warnings before downstream analysis.

Analysis Preparation Checklist

4/6 ready

Group labels reviewed

Blocked

No complete case/control grouping exists yet.

Review the sample grouping table and assign both case and control groups.

Minimum sample count met

Blocked

At least one group has fewer than 2 samples.

Choose a larger dataset or merge only scientifically valid groups.

Processed counts available

Ready

Processed data availability is marked true in the GEO index.

Verify that downloaded processed files contain usable count or expression identifiers.

Ambiguous samples handled

Ready

No review-needed or unassigned samples are present in the proposed grouping.

Review the grouping table for biologically meaningful differences that the automated checks may not detect.

Exclusion decisions recorded

Ready

No hard-excluded samples were detected by the current rules.

Record any manual exclusions in the downstream analysis notes.

Source traceability preserved

Ready

The dataset and sample accessions can be traced back to GEO.

Keep GEO accessions with exported metadata.

Bioinformatician Review

Bioinformatician review required

Ask a bioinformatician to review grouping, count availability, exclusions, and design before DE.

Analysis readiness has blockers that must be resolved before DE.

Analysis preparation checklist contains blocked items.

No complete case/control or treatment/control contrast is available.

At least one comparison group has fewer than two samples.

Critical dataset warnings are present.

Assay context may require expert handling before DESeq2-style analysis.

Study design is model-system or unclear and should be reviewed before analysis.

Why This Is Ranked Here

Tumor vs normal
Not suitable Dataset does not meet the current suitability threshold.

Applied Review Decisions

No active review decisions affect this ranking.

Derived Classifications

  • Assay differs from search intent Microarray Search intent expects bulk RNA-seq. Assay came from Normalization rules.
  • Disease context Fibrosis, liver cancer, liver fibrosis, steatotic liver disease Disease context came from Normalization rules.
  • Likely case group Liver fibrosis 72 samples
  • Likely control group No control group detected 0 samples

Intent Interpretation

  • Downgrade or exclusion reason Comparison: Unclear study design. Specimen: Biopsy. Comparison suitability: 0%. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

  • 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.

Cautions

  • 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.
  • Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
  • Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Missing or unclear metadata. Comparison - Unclear study design. Specimen - Biopsy. Comparison suitability: 0%.
  • Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

Normalized Fields

showing 500 of 511 fields

Sample Group Preview

showing 50 of 72 preview rows
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Study totals: Case 72 | Control 0 | Unassigned 0 | Excluded 0 | Ambiguous 0 showing 50 of 72 preview rows
Group Role Accession Title Source / characteristics Reason
Liver fibrosis Case GSM789110 NAFLD liver biopsy tissue 15004 NAFLD liver biopsy tissue Stage: Advanced (fibrosis stage 3-4); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789111 NAFLD liver biopsy tissue 15006 NAFLD liver biopsy tissue Stage: Advanced (fibrosis stage 3-4); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789112 NAFLD liver biopsy tissue 15010 NAFLD liver biopsy tissue Stage: Mild (fibrosis stage 0-1); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789113 NAFLD liver biopsy tissue 15012 NAFLD liver biopsy tissue Stage: Mild (fibrosis stage 0-1); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789114 NAFLD liver biopsy tissue 15022 NAFLD liver biopsy tissue Stage: Mild (fibrosis stage 0-1); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789115 NAFLD liver biopsy tissue 15023 NAFLD liver biopsy tissue Stage: Advanced (fibrosis stage 3-4); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789116 NAFLD liver biopsy tissue 15029 NAFLD liver biopsy tissue Stage: Mild (fibrosis stage 0-1); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789117 NAFLD liver biopsy tissue 15066 NAFLD liver biopsy tissue Stage: Mild (fibrosis stage 0-1); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789118 NAFLD liver biopsy tissue 15079 NAFLD liver biopsy tissue Stage: Mild (fibrosis stage 0-1); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789119 NAFLD liver biopsy tissue 15102 NAFLD liver biopsy tissue Stage: Advanced (fibrosis stage 3-4); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789120 NAFLD liver biopsy tissue 15103 NAFLD liver biopsy tissue Stage: Mild (fibrosis stage 0-1); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789121 NAFLD liver biopsy tissue 15170 NAFLD liver biopsy tissue Stage: Mild (fibrosis stage 0-1); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789122 NAFLD liver biopsy tissue 15177 NAFLD liver biopsy tissue Stage: Advanced (fibrosis stage 3-4); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789123 NAFLD liver biopsy tissue 15195 NAFLD liver biopsy tissue Stage: Advanced (fibrosis stage 3-4); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789124 NAFLD liver biopsy tissue 15202 NAFLD liver biopsy tissue Stage: Advanced (fibrosis stage 3-4); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789125 NAFLD liver biopsy tissue 15214 NAFLD liver biopsy tissue Stage: Advanced (fibrosis stage 3-4); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789126 NAFLD liver biopsy tissue 15238 NAFLD liver biopsy tissue Stage: Mild (fibrosis stage 0-1); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789127 NAFLD liver biopsy tissue 15251 NAFLD liver biopsy tissue Stage: Advanced (fibrosis stage 3-4); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789128 NAFLD liver biopsy tissue 15262 NAFLD liver biopsy tissue Stage: Advanced (fibrosis stage 3-4); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789129 NAFLD liver biopsy tissue 15271 NAFLD liver biopsy tissue Stage: Mild (fibrosis stage 0-1); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789130 NAFLD liver biopsy tissue 15277 NAFLD liver biopsy tissue Stage: Mild (fibrosis stage 0-1); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789131 NAFLD liver biopsy tissue 15290 NAFLD liver biopsy tissue Stage: Mild (fibrosis stage 0-1); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789132 NAFLD liver biopsy tissue 15298 NAFLD liver biopsy tissue Stage: Advanced (fibrosis stage 3-4); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789133 NAFLD liver biopsy tissue 15311 NAFLD liver biopsy tissue Stage: Advanced (fibrosis stage 3-4); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789134 NAFLD liver biopsy tissue 15341 NAFLD liver biopsy tissue Stage: Mild (fibrosis stage 0-1); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789135 NAFLD liver biopsy tissue 15342 NAFLD liver biopsy tissue Stage: Mild (fibrosis stage 0-1); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789136 NAFLD liver biopsy tissue 15361 NAFLD liver biopsy tissue Stage: Mild (fibrosis stage 0-1); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789137 NAFLD liver biopsy tissue 15367 NAFLD liver biopsy tissue Stage: Mild (fibrosis stage 0-1); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789138 NAFLD liver biopsy tissue 15381 NAFLD liver biopsy tissue Stage: Mild (fibrosis stage 0-1); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789139 NAFLD liver biopsy tissue 15386 NAFLD liver biopsy tissue Stage: Mild (fibrosis stage 0-1); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789140 NAFLD liver biopsy tissue 15399 NAFLD liver biopsy tissue Stage: Advanced (fibrosis stage 3-4); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789141 NAFLD liver biopsy tissue 15400 NAFLD liver biopsy tissue Stage: Mild (fibrosis stage 0-1); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789142 NAFLD liver biopsy tissue 15433 NAFLD liver biopsy tissue Stage: Mild (fibrosis stage 0-1); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789143 NAFLD liver biopsy tissue 15441 NAFLD liver biopsy tissue Stage: Mild (fibrosis stage 0-1); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789144 NAFLD liver biopsy tissue 15442 NAFLD liver biopsy tissue Stage: Mild (fibrosis stage 0-1); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789145 NAFLD liver biopsy tissue 15445 NAFLD liver biopsy tissue Stage: Advanced (fibrosis stage 3-4); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789146 NAFLD liver biopsy tissue 15479 NAFLD liver biopsy tissue Stage: Mild (fibrosis stage 0-1); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789147 NAFLD liver biopsy tissue 15495 NAFLD liver biopsy tissue Stage: Mild (fibrosis stage 0-1); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789148 NAFLD liver biopsy tissue 15503 NAFLD liver biopsy tissue Stage: Advanced (fibrosis stage 3-4); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789149 NAFLD liver biopsy tissue 15554 NAFLD liver biopsy tissue Stage: Mild (fibrosis stage 0-1); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789150 NAFLD liver biopsy tissue 15557 NAFLD liver biopsy tissue Stage: Mild (fibrosis stage 0-1); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789151 NAFLD liver biopsy tissue 15568 NAFLD liver biopsy tissue Stage: Advanced (fibrosis stage 3-4); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789152 NAFLD liver biopsy tissue 15626 NAFLD liver biopsy tissue Stage: Advanced (fibrosis stage 3-4); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789153 NAFLD liver biopsy tissue 15681 NAFLD liver biopsy tissue Stage: Advanced (fibrosis stage 3-4); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789154 NAFLD liver biopsy tissue 15684 NAFLD liver biopsy tissue Stage: Mild (fibrosis stage 0-1); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789155 NAFLD liver biopsy tissue 15707 NAFLD liver biopsy tissue Stage: Advanced (fibrosis stage 3-4); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789156 NAFLD liver biopsy tissue 15742 NAFLD liver biopsy tissue Stage: Mild (fibrosis stage 0-1); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789157 NAFLD liver biopsy tissue 15757 NAFLD liver biopsy tissue Stage: Mild (fibrosis stage 0-1); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789158 NAFLD liver biopsy tissue 15771 NAFLD liver biopsy tissue Stage: Advanced (fibrosis stage 3-4); Tissue: Liver Case marker detected.
Liver fibrosis Case GSM789159 NAFLD liver biopsy tissue 15776 NAFLD liver biopsy tissue Stage: Mild (fibrosis stage 0-1); Tissue: Liver Case marker detected.
22 additional case samples are hidden from this preview.

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