GSE193066

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

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

164 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 from 106 HCC-naive NAFLD patients (164 biopsy tissues, including 1st biopsy for all patients and 2nd follow-up biopsy for 58 PLS-NAFLD high-risk patients), and used for RNA isolation and genome-wide transcriptome profiling by RNA-Seq.

Source Evidence

4 sources
Source Contribution Status
GEO

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

Sample records
164 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.

2 linked publications 2 DOIs

Primary publication

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

Related publications

  1. A FAPα-activated MRI nanoprobe for precise grading diagnosis of clinical liver fibrosis. Nature communications, 2024
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 164 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

  • 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.

Cautions

  • Comparison: Unclear study design. Specimen: Biopsy. 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 - 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 1156 fields

Sample Group Preview

showing 50 of 164 preview rows
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Study totals: Case 164 | Control 0 | Unassigned 0 | Excluded 0 | Ambiguous 0 showing 50 of 164 preview rows
Group Role Accession Title Source / characteristics Reason
Liver fibrosis Case GSM5772501 HUnafld001 HUnafld001 Tissue: Liver; Biopsy: 1st biopsy; Age: 46; Sex: Female; Fibrosis stage: 0; Nafld activity score: 5; Pls-nafld-based risk prediction at 1st biopsy: Low-risk Case marker detected.
Liver fibrosis Case GSM5772502 HUnafld002 HUnafld002 Tissue: Liver; Biopsy: 1st biopsy; Age: 43; Sex: Male; Fibrosis stage: 1; Nafld activity score: 2; Pls-nafld-based risk prediction at 1st biopsy: High-risk Case marker detected.
Liver fibrosis Case GSM5772503 HUnafld003 HUnafld003 Tissue: Liver; Biopsy: 1st biopsy; Age: 65; Sex: Male; Fibrosis stage: 0; Nafld activity score: 3; Pls-nafld-based risk prediction at 1st biopsy: High-risk Case marker detected.
Liver fibrosis Case GSM5772504 HUnafld004 HUnafld004 Tissue: Liver; Biopsy: 1st biopsy; Age: 55; Sex: Male; Fibrosis stage: 1; Nafld activity score: 5; Pls-nafld-based risk prediction at 1st biopsy: High-risk Case marker detected.
Liver fibrosis Case GSM5772505 HUnafld005 HUnafld005 Tissue: Liver; Biopsy: 1st biopsy; Age: 20; Sex: Male; Fibrosis stage: 1; Nafld activity score: 6; Pls-nafld-based risk prediction at 1st biopsy: Low-risk Case marker detected.
Liver fibrosis Case GSM5772506 HUnafld006 HUnafld006 Tissue: Liver; Biopsy: 1st biopsy; Age: 44; Sex: Male; Fibrosis stage: 1; Nafld activity score: 3; Pls-nafld-based risk prediction at 1st biopsy: High-risk Case marker detected.
Liver fibrosis Case GSM5772507 HUnafld007 HUnafld007 Tissue: Liver; Biopsy: 1st biopsy; Age: 31; Sex: Male; Fibrosis stage: 1; Nafld activity score: 5; Pls-nafld-based risk prediction at 1st biopsy: Low-risk Case marker detected.
Liver fibrosis Case GSM5772508 HUnafld008 HUnafld008 Tissue: Liver; Biopsy: 1st biopsy; Age: 48; Sex: Male; Fibrosis stage: 0; Nafld activity score: 6; Pls-nafld-based risk prediction at 1st biopsy: Low-risk Case marker detected.
Liver fibrosis Case GSM5772509 HUnafld009 HUnafld009 Tissue: Liver; Biopsy: 1st biopsy; Age: 62; Sex: Male; Fibrosis stage: 1; Nafld activity score: 2; Pls-nafld-based risk prediction at 1st biopsy: Low-risk Case marker detected.
Liver fibrosis Case GSM5772510 HUnafld010 HUnafld010 Tissue: Liver; Biopsy: 1st biopsy; Age: 74; Sex: Male; Fibrosis stage: 1; Nafld activity score: 3; Pls-nafld-based risk prediction at 1st biopsy: Low-risk Case marker detected.
Liver fibrosis Case GSM5772511 HUnafld011 HUnafld011 Tissue: Liver; Biopsy: 1st biopsy; Age: 71; Sex: Male; Fibrosis stage: 0; Nafld activity score: 3; Pls-nafld-based risk prediction at 1st biopsy: High-risk Case marker detected.
Liver fibrosis Case GSM5772512 HUnafld012 HUnafld012 Tissue: Liver; Biopsy: 1st biopsy; Age: 32; Sex: Male; Fibrosis stage: 0; Nafld activity score: 5; Pls-nafld-based risk prediction at 1st biopsy: Low-risk Case marker detected.
Liver fibrosis Case GSM5772513 HUnafld013 HUnafld013 Tissue: Liver; Biopsy: 1st biopsy; Age: 59; Sex: Male; Fibrosis stage: 0; Nafld activity score: 1; Pls-nafld-based risk prediction at 1st biopsy: Low-risk Case marker detected.
Liver fibrosis Case GSM5772514 HUnafld015 HUnafld015 Tissue: Liver; Biopsy: 1st biopsy; Age: 40; Sex: Female; Fibrosis stage: 1; Nafld activity score: 6; Pls-nafld-based risk prediction at 1st biopsy: Low-risk Case marker detected.
Liver fibrosis Case GSM5772515 HUnafld016 HUnafld016 Tissue: Liver; Biopsy: 1st biopsy; Age: 47; Sex: Male; Fibrosis stage: 1; Nafld activity score: 4; Pls-nafld-based risk prediction at 1st biopsy: Low-risk Case marker detected.
Liver fibrosis Case GSM5772516 HUnafld017 HUnafld017 Tissue: Liver; Biopsy: 1st biopsy; Age: 66; Sex: Male; Fibrosis stage: 1; Nafld activity score: 1; Pls-nafld-based risk prediction at 1st biopsy: High-risk Case marker detected.
Liver fibrosis Case GSM5772517 HUnafld018 HUnafld018 Tissue: Liver; Biopsy: 1st biopsy; Age: 41; Sex: Male; Fibrosis stage: 1; Nafld activity score: 3; Pls-nafld-based risk prediction at 1st biopsy: Low-risk Case marker detected.
Liver fibrosis Case GSM5772518 HUnafld019 HUnafld019 Tissue: Liver; Biopsy: 1st biopsy; Age: 59; Sex: Female; Fibrosis stage: 1; Nafld activity score: 3; Pls-nafld-based risk prediction at 1st biopsy: Low-risk Case marker detected.
Liver fibrosis Case GSM5772519 HUnafld020 HUnafld020 Tissue: Liver; Biopsy: 1st biopsy; Age: 31; Sex: Male; Fibrosis stage: 1; Nafld activity score: 6; Pls-nafld-based risk prediction at 1st biopsy: High-risk Case marker detected.
Liver fibrosis Case GSM5772520 HUnafld021 HUnafld021 Tissue: Liver; Biopsy: 1st biopsy; Age: 51; Sex: Male; Fibrosis stage: 1; Nafld activity score: 4; Pls-nafld-based risk prediction at 1st biopsy: Low-risk Case marker detected.
Liver fibrosis Case GSM5772521 HUnafld023 HUnafld023 Tissue: Liver; Biopsy: 1st biopsy; Age: 31; Sex: Male; Fibrosis stage: 1; Nafld activity score: 4; Pls-nafld-based risk prediction at 1st biopsy: Low-risk Case marker detected.
Liver fibrosis Case GSM5772522 HUnafld024 HUnafld024 Tissue: Liver; Biopsy: 1st biopsy; Age: 57; Sex: Female; Fibrosis stage: 1; Nafld activity score: 6; Pls-nafld-based risk prediction at 1st biopsy: High-risk Case marker detected.
Liver fibrosis Case GSM5772523 HUnafld025 HUnafld025 Tissue: Liver; Biopsy: 1st biopsy; Age: 54; Sex: Female; Fibrosis stage: 1; Nafld activity score: 3; Pls-nafld-based risk prediction at 1st biopsy: Low-risk Case marker detected.
Liver fibrosis Case GSM5772524 HUnafld026 HUnafld026 Tissue: Liver; Biopsy: 1st biopsy; Age: 57; Sex: Female; Fibrosis stage: 1; Nafld activity score: 3; Pls-nafld-based risk prediction at 1st biopsy: High-risk Case marker detected.
Liver fibrosis Case GSM5772525 HUnafld027 HUnafld027 Tissue: Liver; Biopsy: 1st biopsy; Age: 63; Sex: Male; Fibrosis stage: 1; Nafld activity score: 3; Pls-nafld-based risk prediction at 1st biopsy: High-risk Case marker detected.
Liver fibrosis Case GSM5772526 HUnafld029 HUnafld029 Tissue: Liver; Biopsy: 1st biopsy; Age: 51; Sex: Female; Fibrosis stage: 1; Nafld activity score: 3; Pls-nafld-based risk prediction at 1st biopsy: Low-risk Case marker detected.
Liver fibrosis Case GSM5772527 HUnafld034 HUnafld034 Tissue: Liver; Biopsy: 1st biopsy; Age: 62; Sex: Female; Fibrosis stage: 2; Nafld activity score: 5; Pls-nafld-based risk prediction at 1st biopsy: Low-risk Case marker detected.
Liver fibrosis Case GSM5772528 HUnafld035_1 HUnafld035_1 Tissue: Liver; Biopsy: 1st biopsy; Age: 20; Sex: Male; Fibrosis stage: 2; Nafld activity score: 4; Pls-nafld-based risk prediction at 1st biopsy: High-risk Case marker detected.
Liver fibrosis Case GSM5772529 HUnafld036 HUnafld036 Tissue: Liver; Biopsy: 1st biopsy; Age: 39; Sex: Male; Fibrosis stage: 3; Nafld activity score: 4; Pls-nafld-based risk prediction at 1st biopsy: Low-risk Case marker detected.
Liver fibrosis Case GSM5772530 HUnafld037 HUnafld037 Tissue: Liver; Biopsy: 1st biopsy; Age: 45; Sex: Male; Fibrosis stage: 2; Nafld activity score: 3; Pls-nafld-based risk prediction at 1st biopsy: Low-risk Case marker detected.
Liver fibrosis Case GSM5772531 HUnafld038_1 HUnafld038_1 Tissue: Liver; Biopsy: 1st biopsy; Age: 42; Sex: Male; Fibrosis stage: 2; Nafld activity score: 6; Pls-nafld-based risk prediction at 1st biopsy: High-risk Case marker detected.
Liver fibrosis Case GSM5772532 HUnafld039_1 HUnafld039_1 Tissue: Liver; Biopsy: 1st biopsy; Age: 55; Sex: Male; Fibrosis stage: 2; Nafld activity score: 3; Pls-nafld-based risk prediction at 1st biopsy: High-risk Case marker detected.
Liver fibrosis Case GSM5772533 HUnafld040 HUnafld040 Tissue: Liver; Biopsy: 1st biopsy; Age: 55; Sex: Female; Fibrosis stage: 2; Nafld activity score: 3; Pls-nafld-based risk prediction at 1st biopsy: Low-risk Case marker detected.
Liver fibrosis Case GSM5772534 HUnafld041 HUnafld041 Tissue: Liver; Biopsy: 1st biopsy; Age: 41; Sex: Male; Fibrosis stage: 1; Nafld activity score: 4; Pls-nafld-based risk prediction at 1st biopsy: Low-risk Case marker detected.
Liver fibrosis Case GSM5772535 HUnafld042 HUnafld042 Tissue: Liver; Biopsy: 1st biopsy; Age: 62; Sex: Male; Fibrosis stage: 2; Nafld activity score: 3; Pls-nafld-based risk prediction at 1st biopsy: Low-risk Case marker detected.
Liver fibrosis Case GSM5772536 HUnafld043 HUnafld043 Tissue: Liver; Biopsy: 1st biopsy; Age: 36; Sex: Male; Fibrosis stage: 2; Nafld activity score: 4; Pls-nafld-based risk prediction at 1st biopsy: Low-risk Case marker detected.
Liver fibrosis Case GSM5772537 HUnafld044 HUnafld044 Tissue: Liver; Biopsy: 1st biopsy; Age: 42; Sex: Male; Fibrosis stage: 2; Nafld activity score: 3; Pls-nafld-based risk prediction at 1st biopsy: Low-risk Case marker detected.
Liver fibrosis Case GSM5772538 HUnafld045 HUnafld045 Tissue: Liver; Biopsy: 1st biopsy; Age: 64; Sex: Male; Fibrosis stage: 1; Nafld activity score: 2; Pls-nafld-based risk prediction at 1st biopsy: Low-risk Case marker detected.
Liver fibrosis Case GSM5772539 HUnafld046_1 HUnafld046_1 Tissue: Liver; Biopsy: 1st biopsy; Age: 63; Sex: Female; Fibrosis stage: 2; Nafld activity score: 3; Pls-nafld-based risk prediction at 1st biopsy: High-risk Case marker detected.
Liver fibrosis Case GSM5772540 HUnafld047_1 HUnafld047_1 Tissue: Liver; Biopsy: 1st biopsy; Age: 50; Sex: Male; Fibrosis stage: 1; Nafld activity score: 5; Pls-nafld-based risk prediction at 1st biopsy: High-risk Case marker detected.
Liver fibrosis Case GSM5772541 HUnafld048_1 HUnafld048_1 Tissue: Liver; Biopsy: 1st biopsy; Age: 46; Sex: Male; Fibrosis stage: 1; Nafld activity score: 3; Pls-nafld-based risk prediction at 1st biopsy: High-risk Case marker detected.
Liver fibrosis Case GSM5772542 HUnafld049_1 HUnafld049_1 Tissue: Liver; Biopsy: 1st biopsy; Age: 57; Sex: Male; Fibrosis stage: 2; Nafld activity score: 3; Pls-nafld-based risk prediction at 1st biopsy: High-risk Case marker detected.
Liver fibrosis Case GSM5772543 HUnafld050_1 HUnafld050_1 Tissue: Liver; Biopsy: 1st biopsy; Age: 69; Sex: Male; Fibrosis stage: 3; Nafld activity score: 4; Pls-nafld-based risk prediction at 1st biopsy: High-risk Case marker detected.
Liver fibrosis Case GSM5772544 HUnafld051 HUnafld051 Tissue: Liver; Biopsy: 1st biopsy; Age: 52; Sex: Male; Fibrosis stage: 2; Nafld activity score: 3; Pls-nafld-based risk prediction at 1st biopsy: Low-risk Case marker detected.
Liver fibrosis Case GSM5772545 HUnafld052_1 HUnafld052_1 Tissue: Liver; Biopsy: 1st biopsy; Age: 69; Sex: Male; Fibrosis stage: 3; Nafld activity score: 2; Pls-nafld-based risk prediction at 1st biopsy: High-risk Case marker detected.
Liver fibrosis Case GSM5772546 HUnafld053_1 HUnafld053_1 Tissue: Liver; Biopsy: 1st biopsy; Age: 49; Sex: Male; Fibrosis stage: 2; Nafld activity score: 4; Pls-nafld-based risk prediction at 1st biopsy: High-risk Case marker detected.
Liver fibrosis Case GSM5772547 HUnafld054_1 HUnafld054_1 Tissue: Liver; Biopsy: 1st biopsy; Age: 45; Sex: Female; Fibrosis stage: 2; Nafld activity score: 3; Pls-nafld-based risk prediction at 1st biopsy: High-risk Case marker detected.
Liver fibrosis Case GSM5772548 HUnafld055 HUnafld055 Tissue: Liver; Biopsy: 1st biopsy; Age: 50; Sex: Female; Fibrosis stage: 3; Nafld activity score: 7; Pls-nafld-based risk prediction at 1st biopsy: High-risk Case marker detected.
Liver fibrosis Case GSM5772549 HUnafld056_1 HUnafld056_1 Tissue: Liver; Biopsy: 1st biopsy; Age: 60; Sex: Male; Fibrosis stage: 3; Nafld activity score: 7; Pls-nafld-based risk prediction at 1st biopsy: High-risk Case marker detected.
Liver fibrosis Case GSM5772550 HUnafld057_1 HUnafld057_1 Tissue: Liver; Biopsy: 1st biopsy; Age: 68; Sex: Female; Fibrosis stage: 3; Nafld activity score: 4; Pls-nafld-based risk prediction at 1st biopsy: High-risk Case marker detected.
114 additional case samples are hidden from this preview.

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.