GSE193080

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

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

59 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

Total RNA for genome-wide transcriptome profiling by RNA-Seq was extracted from formalin-fixed paraffin embedded tissues of tumor-adjacent liver tissues obtained at the time of curative surgical resection for NAFLD-related HCC.

Source Evidence

4 sources
Source Contribution Status
GEO

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

Sample records
59 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.

4 linked publications 4 DOIs

Primary publication

  1. Disseminative Recurrence Signature for Hepatocellular Carcinoma From Nonalcoholic Fatty Liver Disease. Gastro hep advances, 2023
  2. Molecular signatures of long-term hepatocellular carcinoma risk in nonalcoholic fatty liver disease. Science translational medicine, 2022

Related publications

  1. Exploring Transcriptomic and MRI-Derived Parameters Correlations in NAFLD Fibrosis: Insights from a Rat Model. Digestive diseases and sciences, 2026
  2. 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 59 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 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.

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

303 fields

Sample Group Preview

showing 50 of 59 preview rows
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Study totals: Case 59 | Control 0 | Unassigned 0 | Excluded 0 | Ambiguous 0 showing 50 of 59 preview rows
Group Role Accession Title Source / characteristics Reason
Liver fibrosis Case GSM5772888 KU002a KU002a Tissue: Liver; Age: 36; Sex: Female; Fibrosis stage: 2; Nafld activity score: 0; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5772889 KU012a KU012a Tissue: Liver; Age: 57; Sex: Male; Fibrosis stage: 3; Nafld activity score: 2; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5772890 KU020a KU020a Tissue: Liver; Age: 75; Sex: Female; Fibrosis stage: 1; Nafld activity score: 0; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5772891 KU022a KU022a Tissue: Liver; Age: 77; Sex: Male; Fibrosis stage: 1; Nafld activity score: 3; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5772892 KU039a KU039a Tissue: Liver; Age: 57; Sex: Male; Fibrosis stage: 3; Nafld activity score: 1; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5772893 KU050a KU050a Tissue: Liver; Age: 82; Sex: Male; Fibrosis stage: 3; Nafld activity score: 2; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5772894 KU059a KU059a Tissue: Liver; Age: 72; Sex: Male; Fibrosis stage: 2; Nafld activity score: 4; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5772895 KU061a KU061a Tissue: Liver; Age: 64; Sex: Female; Fibrosis stage: 1; Nafld activity score: 0; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5772896 KU062a KU062a Tissue: Liver; Age: 69; Sex: Male; Fibrosis stage: 1; Nafld activity score: 1; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5772897 KU065a KU065a 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 GSM5772898 KU068a KU068a Tissue: Liver; Age: 44; Sex: Female; Fibrosis stage: 0; Nafld activity score: 2; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5772899 KU069a KU069a Tissue: Liver; Age: 69; Sex: Male; Fibrosis stage: 1; Nafld activity score: 0; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5772900 KU072a KU072a Tissue: Liver; Age: 65; Sex: Male; Fibrosis stage: 3; Nafld activity score: 0; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5772901 KU073a KU073a Tissue: Liver; Age: 56; Sex: Female; Fibrosis stage: 4; Nafld activity score: 5; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5772902 KU074a KU074a Tissue: Liver; Age: 72; Sex: Male; Fibrosis stage: 3; Nafld activity score: 0; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5772903 KU075a KU075a Tissue: Liver; Age: 77; Sex: Male; Fibrosis stage: 2; Nafld activity score: 3; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5772904 KU076a KU076a Tissue: Liver; Age: 76; Sex: Female; Fibrosis stage: 2; Nafld activity score: 0; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5772905 KU077a KU077a Tissue: Liver; Age: 59; Sex: Male; Fibrosis stage: 0; Nafld activity score: 0; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5772906 KU078a KU078a Tissue: Liver; Age: 77; Sex: Male; Fibrosis stage: 1; Nafld activity score: 0; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5772907 KU079a KU079a Tissue: Liver; Age: 79; Sex: Female; Fibrosis stage: 4; Nafld activity score: 3; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5772908 KU081a KU081a Tissue: Liver; Age: 63; Sex: Male; Fibrosis stage: 3; Nafld activity score: 0; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5772909 KU085a KU085a Tissue: Liver; Age: 76; Sex: Male; Fibrosis stage: 1; Nafld activity score: 2; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5772910 KU086a KU086a Tissue: Liver; Age: 65; Sex: Male; Fibrosis stage: 3; Nafld activity score: 0; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5772911 KU087a KU087a Tissue: Liver; Age: 65; Sex: Male; Fibrosis stage: 3; Nafld activity score: 2; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5772912 KU088a KU088a Tissue: Liver; Age: 72; Sex: Male; Fibrosis stage: 4; Nafld activity score: 1; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5772913 KU089a KU089a Tissue: Liver; Age: 75; Sex: Male; Fibrosis stage: 1; Nafld activity score: 0; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5772914 KU091a KU091a Tissue: Liver; Age: 77; Sex: Male; Fibrosis stage: 3; Nafld activity score: 0; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5772915 KU092a KU092a Tissue: Liver; Age: 73; Sex: Male; Fibrosis stage: 1; Nafld activity score: 1; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5772916 KU093a KU093a Tissue: Liver; Age: 60; Sex: Female; Fibrosis stage: 0; Nafld activity score: 2; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5772917 KU095a KU095a Tissue: Liver; Age: 68; Sex: Male; Fibrosis stage: 4; Nafld activity score: 3; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5772918 KU097a KU097a Tissue: Liver; Age: 70; Sex: Male; Fibrosis stage: 0; Nafld activity score: 0; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5772919 KU100a KU100a Tissue: Liver; Age: 69; Sex: Female; Fibrosis stage: 4; Nafld activity score: 6; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5772920 KU101a KU101a Tissue: Liver; Age: 72; Sex: Female; Fibrosis stage: 3; Nafld activity score: 0; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5772921 KU102a KU102a 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 GSM5772922 KU106a KU106a Tissue: Liver; Age: 74; Sex: Male; Fibrosis stage: 2; Nafld activity score: 1; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5772923 KU107a KU107a Tissue: Liver; Age: 68; Sex: Male; Fibrosis stage: 1; Nafld activity score: 0; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5772924 KU109a KU109a Tissue: Liver; Age: 79; Sex: Male; Fibrosis stage: 2; Nafld activity score: 4; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5772925 KU111a KU111a Tissue: Liver; Age: 63; Sex: Female; Fibrosis stage: 1; Nafld activity score: 0; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5772926 KU113a KU113a Tissue: Liver; Age: 78; Sex: Female; Fibrosis stage: 2; Nafld activity score: 0; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5772927 KU115a KU115a Tissue: Liver; Age: 74; Sex: Male; Fibrosis stage: 4; Nafld activity score: 3; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5772928 KU116a KU116a Tissue: Liver; Age: 82; Sex: Male; Fibrosis stage: 1; Nafld activity score: 0; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5772929 KU118a KU118a Tissue: Liver; Age: 77; Sex: Male; Fibrosis stage: 1; Nafld activity score: 0; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5772930 KU119a KU119a Tissue: Liver; Age: 79; Sex: Male; Fibrosis stage: 1; Nafld activity score: 5; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5772931 KU120a KU120a Tissue: Liver; Age: 63; Sex: Male; Fibrosis stage: 1; Nafld activity score: 0; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5772932 KU121a KU121a Tissue: Liver; Age: 69; Sex: Male; Fibrosis stage: 3; Nafld activity score: 3; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5772933 KU122a KU122a Tissue: Liver; Age: 79; Sex: Female; Fibrosis stage: 1; Nafld activity score: 0; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5772934 KU124a KU124a Tissue: Liver; Age: 58; Sex: Male; Fibrosis stage: 1; Nafld activity score: 1; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5772935 KU126a KU126a Tissue: Liver; Age: 84; Sex: Male; Fibrosis stage: 1; Nafld activity score: 0; Pls-nafld-based risk prediction: High-risk Case marker detected.
Liver fibrosis Case GSM5772936 KU128a KU128a Tissue: Liver; Age: 75; Sex: Male; Fibrosis stage: 4; Nafld activity score: 2; Pls-nafld-based risk prediction: Low-risk Case marker detected.
Liver fibrosis Case GSM5772937 KU130a KU130a Tissue: Liver; Age: 81; Sex: Female; Fibrosis stage: 2; Nafld activity score: 1; Pls-nafld-based risk prediction: High-risk Case marker detected.
9 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.