GSE11536

Mild vs advanced liver fibrosis

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

The aim of this study is to compare mild and advanced liver fibrosis gene expression profiling and to identify novel markers of fibrosis progression. By transcriptome analysis with a cDNA array virtually covering every transcript in liver, we compared transcript levels in mild (F1 Metavir score) and advanced (F4 Metavir score) fibrosis. A stringent selection identified a list of 16 transcripts which completely separated the 2 groups of patients (8 F1 and 8 F4). We report that dysregulations at the transcriptional level do exist between mild fibrosis (F1) and advanced fibrosis (F4). Keywords: fibrosis stage-dependent analysis

Overall design

Fibrosis samples were analyzed for 16 patients : 8 mild fibrosis (F1-1 to F1-8) and 8 advanced fibrosis (F4-1 to F4-8). All data in the current study were obtained from 3 separate hybridizations per RNA sample.

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. Novel serum markers of fibrosis progression for the follow-up of hepatitis C virus-infected patients. The American journal of pathology, 2009
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 fibrosis 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

  • 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.
  • Publication context: Novel serum markers of fibrosis progression for the follow-up of hepatitis C virus-infected patients.. The American journal of pathology, 2009. PMID 19477948. DOI 10.2353/ajpath.2009.080850.

Cautions

  • Comparison: Unclear study design. Specimen: Tissue. 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 - 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

197 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 GSM290574 Fibrosis F1 - patient 1 -hyb 1 Liver fibrosis - Metavir score : F1, mild fibrosis Age: 34 years old; Sex: Male; HCV-infected Case marker detected.
Liver fibrosis Case GSM290575 Fibrosis F1 - patient 1 -hyb 2 Liver fibrosis - Metavir score : F1, mild fibrosis Age: 34 years old; Sex: Male; HCV-infected Case marker detected.
Liver fibrosis Case GSM290576 Fibrosis F1 - patient 1 -hyb 3 Liver fibrosis - Metavir score : F1, mild fibrosis Age: 34 years old; Sex: Male; HCV-infected Case marker detected.
Liver fibrosis Case GSM290577 Fibrosis F1 - patient 2 -hyb 1 Liver fibrosis - Metavir score : F1, mild fibrosis Age: 61 years old; Sex: Female; HCV-infected Case marker detected.
Liver fibrosis Case GSM290578 Fibrosis F1 - patient 2 -hyb 2 Liver fibrosis - Metavir score : F1, mild fibrosis Age: 61 years old; Sex: Female; HCV-infected Case marker detected.
Liver fibrosis Case GSM290579 Fibrosis F1 - patient 2 -hyb 3 Liver fibrosis - Metavir score : F1, mild fibrosis Age: 61 years old; Sex: Female; HCV-infected Case marker detected.
Liver fibrosis Case GSM290580 Fibrosis F1 - patient 3 -hyb 1 Liver fibrosis - Metavir score : F1, mild fibrosis Age: 50 years old; Sex: Female; HCV-infected Case marker detected.
Liver fibrosis Case GSM290581 Fibrosis F1 - patient 3 -hyb 2 Liver fibrosis - Metavir score : F1, mild fibrosis Age: 50 years old; Sex: Female; HCV-infected Case marker detected.
Liver fibrosis Case GSM290582 Fibrosis F1 - patient 3 -hyb 3 Liver fibrosis - Metavir score : F1, mild fibrosis Age: 50 years old; Sex: Female; HCV-infected Case marker detected.
Liver fibrosis Case GSM290583 Fibrosis F1 - patient 4 -hyb 1 Liver fibrosis - Metavir score : F1, mild fibrosis Age: 41 years old; Sex: Male; HCV-infected Case marker detected.
Liver fibrosis Case GSM290584 Fibrosis F1 - patient 4 -hyb 2 Liver fibrosis - Metavir score : F1, mild fibrosis Age: 41 years old; Sex: Male; HCV-infected Case marker detected.
Liver fibrosis Case GSM290585 Fibrosis F1 - patient 4 -hyb 3 Liver fibrosis - Metavir score : F1, mild fibrosis Age: 41 years old; Sex: Male; HCV-infected Case marker detected.
Liver fibrosis Case GSM290586 Fibrosis F1 - patient 5 -hyb 1 Liver fibrosis - Metavir score : F1, mild fibrosis Age: 54 years old; Sex: Female; HCV-infected Case marker detected.
Liver fibrosis Case GSM290587 Fibrosis F1 - patient 5 -hyb 2 Liver fibrosis - Metavir score : F1, mild fibrosis Age: 54 years old; Sex: Female; HCV-infected Case marker detected.
Liver fibrosis Case GSM290588 Fibrosis F1 - patient 5 -hyb 3 Liver fibrosis - Metavir score : F1, mild fibrosis Age: 54 years old; Sex: Female; HCV-infected Case marker detected.
Liver fibrosis Case GSM290589 Fibrosis F1 - patient 6 -hyb 1 Liver fibrosis - Metavir score : F1, mild fibrosis Age: 65 years old; Sex: Male; HCV-infected Case marker detected.
Liver fibrosis Case GSM290590 Fibrosis F1 - patient 6 -hyb 2 Liver fibrosis - Metavir score : F1, mild fibrosis Age: 65 years old; Sex: Male; HCV-infected Case marker detected.
Liver fibrosis Case GSM290591 Fibrosis F1 - patient 6 -hyb 3 Liver fibrosis - Metavir score : F1, mild fibrosis Age: 65 years old; Sex: Male; HCV-infected Case marker detected.
Liver fibrosis Case GSM290592 Fibrosis F1 - patient 7 -hyb 1 Liver fibrosis - Metavir score : F1, mild fibrosis Age: 37 years old; Sex: Female; HCV-infected Case marker detected.
Liver fibrosis Case GSM290593 Fibrosis F1 - patient 7 -hyb 2 Liver fibrosis - Metavir score : F1, mild fibrosis Age: 37 years old; Sex: Female; HCV-infected Case marker detected.
Liver fibrosis Case GSM290594 Fibrosis F1 - patient 7 -hyb 3 Liver fibrosis - Metavir score : F1, mild fibrosis Age: 37 years old; Sex: Female; HCV-infected Case marker detected.
Liver fibrosis Case GSM290595 Fibrosis F1 - patient 8 -hyb 1 Liver fibrosis - Metavir score : F1, mild fibrosis Age: 39 years old; Sex: Female; HCV-infected Case marker detected.
Liver fibrosis Case GSM290596 Fibrosis F1 - patient 8 -hyb 2 Liver fibrosis - Metavir score : F1, mild fibrosis Age: 39 years old; Sex: Female; HCV-infected Case marker detected.
Liver fibrosis Case GSM290597 Fibrosis F1 - patient 8 -hyb 3 Liver fibrosis - Metavir score : F1, mild fibrosis Age: 39 years old; Sex: Female; HCV-infected Case marker detected.
Liver fibrosis Case GSM290598 Fibrosis F4 - patient 1 -hyb 1 Liver fibrosis - Metavir score : F4, advanced fibrosis Age: 68 years old; Sex: Male; HCV-infected Case marker detected.
Liver fibrosis Case GSM290599 Fibrosis F4 - patient 1 -hyb 2 Liver fibrosis - Metavir score : F4, advanced fibrosis Age: 68 years old; Sex: Male; HCV-infected Case marker detected.
Liver fibrosis Case GSM290600 Fibrosis F4 - patient 1 -hyb 3 Liver fibrosis - Metavir score : F4, advanced fibrosis Age: 68 years old; Sex: Male; HCV-infected Case marker detected.
Liver fibrosis Case GSM290601 Fibrosis F4 - patient 2 -hyb 1 Liver fibrosis - Metavir score : F4, advanced fibrosis Age: 69 years old; Sex: Male; HCV-infected Case marker detected.
Liver fibrosis Case GSM290602 Fibrosis F4 - patient 2 -hyb 2 Liver fibrosis - Metavir score : F4, advanced fibrosis Age: 69 years old; Sex: Male; HCV-infected Case marker detected.
Liver fibrosis Case GSM290603 Fibrosis F4 - patient 2 -hyb 3 Liver fibrosis - Metavir score : F4, advanced fibrosis Age: 69 years old; Sex: Male; HCV-infected Case marker detected.
Liver fibrosis Case GSM290604 Fibrosis F4 - patient 3 -hyb 1 Liver fibrosis - Metavir score : F4, advanced fibrosis Age: 57 years old; Sex: Male; HCV-infected Case marker detected.
Liver fibrosis Case GSM290605 Fibrosis F4 - patient 3 -hyb 2 Liver fibrosis - Metavir score : F4, advanced fibrosis Age: 57 years old; Sex: Male; HCV-infected Case marker detected.
Liver fibrosis Case GSM290606 Fibrosis F4 - patient 3 -hyb 3 Liver fibrosis - Metavir score : F4, advanced fibrosis Age: 57 years old; Sex: Male; HCV-infected Case marker detected.
Liver fibrosis Case GSM290607 Fibrosis F4 - patient 4 -hyb 1 Liver fibrosis - Metavir score : F4, advanced fibrosis Age: 55 years old; Sex: Male; HCV-infected Case marker detected.
Liver fibrosis Case GSM290608 Fibrosis F4 - patient 4 -hyb 2 Liver fibrosis - Metavir score : F4, advanced fibrosis Age: 55 years old; Sex: Male; HCV-infected Case marker detected.
Liver fibrosis Case GSM290609 Fibrosis F4 - patient 4 -hyb 3 Liver fibrosis - Metavir score : F4, advanced fibrosis Age: 55 years old; Sex: Male; HCV-infected Case marker detected.
Liver fibrosis Case GSM290610 Fibrosis F4 - patient 5 -hyb 1 Liver fibrosis - Metavir score : F4, advanced fibrosis Age: 20 years old; Sex: Male; HCV-infected Case marker detected.
Liver fibrosis Case GSM290611 Fibrosis F4 - patient 5 -hyb 2 Liver fibrosis - Metavir score : F4, advanced fibrosis Age: 20 years old; Sex: Male; HCV-infected Case marker detected.
Liver fibrosis Case GSM290612 Fibrosis F4 - patient 5 -hyb 3 Liver fibrosis - Metavir score : F4, advanced fibrosis Age: 20 years old; Sex: Male; HCV-infected Case marker detected.
Liver fibrosis Case GSM290613 Fibrosis F4 - patient 6 -hyb 1 Liver fibrosis - Metavir score : F4, advanced fibrosis Age: 58 years old; Sex: Female; HCV-infected Case marker detected.
Liver fibrosis Case GSM290614 Fibrosis F4 - patient 6 -hyb 2 Liver fibrosis - Metavir score : F4, advanced fibrosis Age: 58 years old; Sex: Female; HCV-infected Case marker detected.
Liver fibrosis Case GSM290615 Fibrosis F4 - patient 6 -hyb 3 Liver fibrosis - Metavir score : F4, advanced fibrosis Age: 58 years old; Sex: Female; HCV-infected Case marker detected.
Liver fibrosis Case GSM290616 Fibrosis F4 - patient 7 -hyb 1 Liver fibrosis - Metavir score : F4, advanced fibrosis Age: 63 years old; Sex: Female; HCV-infected Case marker detected.
Liver fibrosis Case GSM290617 Fibrosis F4 - patient 7 -hyb 2 Liver fibrosis - Metavir score : F4, advanced fibrosis Age: 63 years old; Sex: Female; HCV-infected Case marker detected.
Liver fibrosis Case GSM290618 Fibrosis F4 - patient 7 -hyb 3 Liver fibrosis - Metavir score : F4, advanced fibrosis Age: 63 years old; Sex: Female; HCV-infected Case marker detected.
Liver fibrosis Case GSM290619 Fibrosis F4 - patient 8 -hyb 1 Liver fibrosis - Metavir score : F4, advanced fibrosis Age: 41 years old; Sex: Male; HCV-infected Case marker detected.
Liver fibrosis Case GSM290620 Fibrosis F4 - patient 8 -hyb 2 Liver fibrosis - Metavir score : F4, advanced fibrosis Age: 41 years old; Sex: Male; HCV-infected Case marker detected.
Liver fibrosis Case GSM290621 Fibrosis F4 - patient 8 -hyb 3 Liver fibrosis - Metavir score : F4, advanced fibrosis Age: 41 years old; Sex: Male; HCV-infected 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.