GSE192959

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

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

48 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

Non-alcoholic fatty liver disease (NAFLD) is a major global health problem with its high prevalence and risk of developing lethal complications, progressive liver fibrosis and hepatocellular carcinoma (HCC), the only rising cancer mortality in the U.S. For early HCC detection to improve the dismal prognosis, there is an urgent unmet need to identify a subset of NAFLD patients with elevated risk of HCC. Herein, we derived a hepatic-transcriptome-based NAFLD-specific HCC risk biomarker, PLS-NAFLD, and validated it in two independent cohorts of HCC-naive and experienced NAFLD patients..

Overall design

Liver biopsy tissues were obtained at the time of ablating NAFLD-related HCC tumors and subjected for RNA isolation and genome-wide transcriptome profiling with RNA-Seq.

Source Evidence

4 sources
Source Contribution Status
GEO

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

Sample records
48 GSM samples
Primary source
recount3

Planned trusted source for processed count availability.

No match found
Expression Atlas

Planned source for curated expression experiment links.

No match found
PubMed

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

1 linked publication 1 DOI

Primary publication

  1. Molecular signatures of long-term hepatocellular carcinoma risk in nonalcoholic fatty liver disease. Science translational medicine, 2022
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.

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

  • Disease context Alcoholic liver disease, fibrosis, hepatocellular carcinoma, liver fibrosis, steatotic liver disease Disease context came from Normalization rules.
  • Likely case group Liver fibrosis 48 samples
  • Likely control group No control group detected 0 samples

Intent Interpretation

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

Ranking Facts

Supporting evidence

  • 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.

Cautions

  • Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%.
  • Downgraded for tissue search because study design or specimen source is unclear.
  • 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 - Tissue. 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

248 fields

Sample Group Preview

48 rows shown
Show Hide
Study totals: Case 48 | Control 0 | Unassigned 0 | Excluded 0 | Ambiguous 0 48 rows shown
Group Role Accession Title Source / characteristics Reason
Liver fibrosis Case GSM5769797 TUnafld001 TUnafld001 Tissue: Liver; Age: 69; Sex: Female; Fibrosis stage: 4; Nafld activity score: 4; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5769798 TUnafld003 TUnafld003 Tissue: Liver; Age: 62; Sex: Male; Fibrosis stage: 2; Nafld activity score: 3; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5769799 TUnafld004 TUnafld004 Tissue: Liver; Age: 67; Sex: Male; Fibrosis stage: 3; Nafld activity score: 3; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5769800 TUnafld005 TUnafld005 Tissue: Liver; Age: 71; Sex: Female; Fibrosis stage: 4; Nafld activity score: 4; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5769801 TUnafld006 TUnafld006 Tissue: Liver; Age: 73; Sex: Female; Fibrosis stage: 4; Nafld activity score: 2; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5769802 TUnafld007 TUnafld007 Tissue: Liver; Age: 74; Sex: Male; Fibrosis stage: 4; Nafld activity score: 5; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5769803 TUnafld008 TUnafld008 Tissue: Liver; Age: 67; Sex: Male; Fibrosis stage: 4; Nafld activity score: 5; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5769804 TUnafld009 TUnafld009 Tissue: Liver; Age: 78; Sex: Female; Fibrosis stage: 3; Nafld activity score: 2; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5769805 TUnafld010 TUnafld010 Tissue: Liver; Age: 80; Sex: Female; Fibrosis stage: 4; Nafld activity score: 5; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5769806 TUnafld011 TUnafld011 Tissue: Liver; Age: 76; Sex: Male; Fibrosis stage: 4; Nafld activity score: 4; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5769807 TUnafld012 TUnafld012 Tissue: Liver; Age: 74; Sex: Female; Fibrosis stage: 3; Nafld activity score: 3; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5769808 TUnafld013 TUnafld013 Tissue: Liver; Age: 75; Sex: Female; Fibrosis stage: 4; Nafld activity score: 1; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5769809 TUnafld014 TUnafld014 Tissue: Liver; Age: 78; Sex: Female; Fibrosis stage: 4; Nafld activity score: 3; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5769810 TUnafld015 TUnafld015 Tissue: Liver; Age: 84; Sex: Male; Fibrosis stage: 3; Nafld activity score: 6; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5769811 TUnafld016 TUnafld016 Tissue: Liver; Age: 77; Sex: Male; Fibrosis stage: 0; Nafld activity score: 2; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5769812 TUnafld017 TUnafld017 Tissue: Liver; Age: 77; Sex: Female; Fibrosis stage: 4; Nafld activity score: 4; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5769813 TUnafld018 TUnafld018 Tissue: Liver; Age: 74; Sex: Male; Fibrosis stage: 3; Nafld activity score: 3; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5769814 TUnafld019 TUnafld019 Tissue: Liver; Age: 80; Sex: Female; Fibrosis stage: 3; Nafld activity score: 2; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5769815 TUnafld020 TUnafld020 Tissue: Liver; Age: 65; Sex: Female; Fibrosis stage: 4; Nafld activity score: 5; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5769816 TUnafld021 TUnafld021 Tissue: Liver; Age: 64; Sex: Male; Fibrosis stage: 2; Nafld activity score: 1; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5769817 TUnafld022 TUnafld022 Tissue: Liver; Age: 56; Sex: Male; Fibrosis stage: 3; Nafld activity score: 3; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5769818 TUnafld023 TUnafld023 Tissue: Liver; Age: 74; Sex: Female; Fibrosis stage: 4; Nafld activity score: 4; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5769819 TUnafld024 TUnafld024 Tissue: Liver; Age: 75; Sex: Female; Fibrosis stage: 4; Nafld activity score: 5; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5769820 TUnafld025 TUnafld025 Tissue: Liver; Age: 74; Sex: Male; Fibrosis stage: 3; Nafld activity score: 3; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5769821 TUnafld026 TUnafld026 Tissue: Liver; Age: 74; Sex: Female; Fibrosis stage: 4; Nafld activity score: 4; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5769822 TUnafld027 TUnafld027 Tissue: Liver; Age: 63; Sex: Female; Fibrosis stage: 4; Nafld activity score: 3; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5769823 TUnafld028 TUnafld028 Tissue: Liver; Age: 72; Sex: Female; Fibrosis stage: 4; Nafld activity score: 3; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5769824 TUnafld029 TUnafld029 Tissue: Liver; Age: 63; Sex: Male; Fibrosis stage: 3; Nafld activity score: 2; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5769825 TUnafld030 TUnafld030 Tissue: Liver; Age: 72; Sex: Female; Fibrosis stage: 1; Nafld activity score: 2; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5769826 TUnafld031 TUnafld031 Tissue: Liver; Age: 73; Sex: Female; Fibrosis stage: 4; Nafld activity score: 3; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5769827 TUnafld032 TUnafld032 Tissue: Liver; Age: 74; Sex: Female; Fibrosis stage: 3; Nafld activity score: 0; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5769828 TUnafld034 TUnafld034 Tissue: Liver; Age: 79; Sex: Female; Fibrosis stage: 3; Nafld activity score: 2; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5769829 TUnafld035 TUnafld035 Tissue: Liver; Age: 76; Sex: Female; Fibrosis stage: 4; Nafld activity score: 5; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5769830 TUnafld037 TUnafld037 Tissue: Liver; Age: 68; Sex: Female; Fibrosis stage: 4; Nafld activity score: 5; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5769831 TUnafld038 TUnafld038 Tissue: Liver; Age: 66; Sex: Female; Fibrosis stage: 3; Nafld activity score: 4; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5769832 TUnafld039 TUnafld039 Tissue: Liver; Age: 64; Sex: Male; Fibrosis stage: 4; Nafld activity score: 4; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5769833 TUnafld040 TUnafld040 Tissue: Liver; Age: 66; Sex: Female; Fibrosis stage: 3; Nafld activity score: 1; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5769834 TUnafld041 TUnafld041 Tissue: Liver; Age: 77; Sex: Female; Fibrosis stage: 4; Nafld activity score: 3; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5769835 TUnafld044 TUnafld044 Tissue: Liver; Age: 73; Sex: Female; Fibrosis stage: 3; Nafld activity score: 2; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5769836 TUnafld045 TUnafld045 Tissue: Liver; Age: 61; Sex: Female; Fibrosis stage: 4; Nafld activity score: 3; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5769837 TUnafld046 TUnafld046 Tissue: Liver; Age: 63; Sex: Male; Fibrosis stage: 4; Nafld activity score: 5; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5769838 TUnafld048 TUnafld048 Tissue: Liver; Age: 71; Sex: Female; Fibrosis stage: 3; Nafld activity score: 5; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5769839 TUnafld050 TUnafld050 Tissue: Liver; Age: 68; Sex: Female; Fibrosis stage: 4; Nafld activity score: 1; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5769840 TUnafld052 TUnafld052 Tissue: Liver; Age: 66; Sex: Female; Fibrosis stage: 4; Nafld activity score: 5; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5769841 TUnafld055 TUnafld055 Tissue: Liver; Age: 71; Sex: Female; Fibrosis stage: 4; Nafld activity score: 5; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5769842 TUnafld059 TUnafld059 Tissue: Liver; Age: 76; Sex: Female; Fibrosis stage: 4; Nafld activity score: 4; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5769843 TUnafld060 TUnafld060 Tissue: Liver; Age: 70; Sex: Male; Fibrosis stage: 2; Nafld activity score: 2; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5769844 TUnafld061 TUnafld061 Tissue: Liver; Age: 70; Sex: Male; Fibrosis stage: 3; Nafld activity score: 2; Pls-nafld-based risk prediction: Low-risk Case marker detected.

Use as Discovery Cohort

External Validation Finder

Carry Siftome's disease, organism, specimen, assay, data type, and accession into a validation project. Uncertain fields remain Unknown.