GSE118587

Expression data for participants in iWITH study at screening visit

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

133 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

A cross sectional study using data collected at the time of liver biopsy, the final eligibility assessment for participation in iWITH (NCT01638559), an immunosuppression withdrawal trial. Microarrays were used to understand the gene expression profile differences among the three histological clusters (Cluster 1, Cluster 2 and Cluster 3)

Overall design

RNA samples (n=151) were extracted from cryopreserved liver tissue samples using TRIzol and hybrid-ized onto Affymetrix Human Genome U219 96-array plates. We performed quality control using AffyPLM and excluded samples with a Normal-ized Unscaled Standard Error >1.05, resulting in 133 evaluable arrays.

Source Evidence

4 sources
Source Contribution Status
GEO

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

Sample records
133 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. Evidence of Chronic Allograft Injury in Liver Biopsies From Long-term Pediatric Recipients of Liver Transplants. Gastroenterology, 2018
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 Inflamed tissue 133 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 fibrosis.
  • Processed data is available for downstream review.
  • External evidence: PubMed links 1 publication; 1 DOI available: PMID 30144432.
  • Publication context: Evidence of Chronic Allograft Injury in Liver Biopsies From Long-term Pediatric Recipients of Liver Transplants.. Gastroenterology, 2018. PMID 30144432. DOI 10.1053/j.gastro.2018.08.023.

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.
  • Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
  • 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 934 fields

Sample Group Preview

showing 50 of 133 preview rows
Show Hide
Study totals: Case 133 | Control 0 | Unassigned 0 | Excluded 0 | Ambiguous 0 showing 50 of 133 preview rows
Group Role Accession Title Source / characteristics Reason
Inflamed tissue Case GSM3333765 SAMPLE 1 Screening Visit_Cluster 2 Tissue: Liver Biopsy; Histological clusters: Cluster 2; Interface activity: None; Perivenular fibrosis: Mild; Ishak fibrosis stage: 2; Lobular inflammation: None; Portal inflammation: None Case marker detected.
Inflamed tissue Case GSM3333766 SAMPLE 2 Screening Visit_Cluster 2 Tissue: Liver Biopsy; Histological clusters: Cluster 2; Interface activity: None; Perivenular fibrosis: None; Ishak fibrosis stage: 2; Lobular inflammation: None; Portal inflammation: Mild Case marker detected.
Inflamed tissue Case GSM3333767 SAMPLE 3 Screening Visit_Cluster 3 Tissue: Liver Biopsy; Histological clusters: Cluster 3; Interface activity: None; Perivenular fibrosis: Mild; Ishak fibrosis stage: 1; Lobular inflammation: None; Portal inflammation: Mild Case marker detected.
Inflamed tissue Case GSM3333768 SAMPLE 4 Screening Visit_Cluster 3 Tissue: Liver Biopsy; Histological clusters: Cluster 3; Interface activity: None; Perivenular fibrosis: None; Ishak fibrosis stage: 1; Lobular inflammation: None; Portal inflammation: None Case marker detected.
Inflamed tissue Case GSM3333769 SAMPLE 5 Screening Visit_Cluster 1 Tissue: Liver Biopsy; Histological clusters: Cluster 1; Interface activity: Mild; Perivenular fibrosis: Mild; Ishak fibrosis stage: 3; Lobular inflammation: None; Portal inflammation: Mild Case marker detected.
Inflamed tissue Case GSM3333770 SAMPLE 6 Screening Visit_Cluster 3 Tissue: Liver Biopsy; Histological clusters: Cluster 3; Interface activity: None; Perivenular fibrosis: Mild; Ishak fibrosis stage: 1; Lobular inflammation: None; Portal inflammation: None Case marker detected.
Inflamed tissue Case GSM3333771 SAMPLE 7 Screening Visit_Cluster 1 Tissue: Liver Biopsy; Histological clusters: Cluster 1; Interface activity: Mild; Perivenular fibrosis: None; Ishak fibrosis stage: 1; Lobular inflammation: Mild; Portal inflammation: Mild Case marker detected.
Inflamed tissue Case GSM3333772 SAMPLE 8 Screening Visit_Cluster 3 Tissue: Liver Biopsy; Histological clusters: Cluster 3; Interface activity: None; Perivenular fibrosis: None; Ishak fibrosis stage: 1; Lobular inflammation: None; Portal inflammation: Mild Case marker detected.
Inflamed tissue Case GSM3333773 SAMPLE 9 Screening Visit_Cluster 1 Tissue: Liver Biopsy; Histological clusters: Cluster 1; Interface activity: Mild; Perivenular fibrosis: None; Ishak fibrosis stage: 2; Lobular inflammation: Mild; Portal inflammation: Moderate Case marker detected.
Inflamed tissue Case GSM3333774 SAMPLE10 Screening Visit_Cluster 2 Tissue: Liver Biopsy; Histological clusters: Cluster 2; Interface activity: None; Perivenular fibrosis: Moderate; Ishak fibrosis stage: 3; Lobular inflammation: None; Portal inflammation: Mild Case marker detected.
Inflamed tissue Case GSM3333775 SAMPLE 11 Screening Visit_Cluster 3 Tissue: Liver Biopsy; Histological clusters: Cluster 3; Interface activity: None; Perivenular fibrosis: None; Ishak fibrosis stage: 1; Lobular inflammation: None; Portal inflammation: Mild Case marker detected.
Inflamed tissue Case GSM3333776 SAMPLE 12 Screening Visit_Cluster 2 Tissue: Liver Biopsy; Histological clusters: Cluster 2; Interface activity: None; Perivenular fibrosis: Mild; Ishak fibrosis stage: 3; Lobular inflammation: None; Portal inflammation: None Case marker detected.
Inflamed tissue Case GSM3333777 SAMPLE 13 Screening Visit_Cluster 3 Tissue: Liver Biopsy; Histological clusters: Cluster 3; Interface activity: None; Perivenular fibrosis: None; Ishak fibrosis stage: 1; Lobular inflammation: None; Portal inflammation: Mild Case marker detected.
Inflamed tissue Case GSM3333778 SAMPLE 14 Screening Visit_Cluster 3 Tissue: Liver Biopsy; Histological clusters: Cluster 3; Interface activity: None; Perivenular fibrosis: Mild; Ishak fibrosis stage: 1; Lobular inflammation: None; Portal inflammation: None Case marker detected.
Inflamed tissue Case GSM3333779 SAMPLE 15 Screening Visit_Cluster 2 Tissue: Liver Biopsy; Histological clusters: Cluster 2; Interface activity: None; Perivenular fibrosis: None; Ishak fibrosis stage: 3; Lobular inflammation: None; Portal inflammation: None Case marker detected.
Inflamed tissue Case GSM3333780 SAMPLE 16 Screening Visit_Cluster 2 Tissue: Liver Biopsy; Histological clusters: Cluster 2; Interface activity: None; Perivenular fibrosis: Mild; Ishak fibrosis stage: 3; Lobular inflammation: None; Portal inflammation: Mild Case marker detected.
Inflamed tissue Case GSM3333781 SAMPLE 17 Screening Visit_Cluster 3 Tissue: Liver Biopsy; Histological clusters: Cluster 3; Interface activity: None; Perivenular fibrosis: None; Ishak fibrosis stage: 1; Lobular inflammation: Mild; Portal inflammation: Mild Case marker detected.
Inflamed tissue Case GSM3333782 SAMPLE 18 Screening Visit_Cluster 3 Tissue: Liver Biopsy; Histological clusters: Cluster 3; Interface activity: None; Perivenular fibrosis: None; Ishak fibrosis stage: 1; Lobular inflammation: None; Portal inflammation: Mild Case marker detected.
Inflamed tissue Case GSM3333783 SAMPLE 19 Screening Visit_Cluster 3 Tissue: Liver Biopsy; Histological clusters: Cluster 3; Interface activity: None; Perivenular fibrosis: Mild; Ishak fibrosis stage: 1; Lobular inflammation: None; Portal inflammation: None Case marker detected.
Inflamed tissue Case GSM3333784 SAMPLE 20 Screening Visit_Cluster 3 Tissue: Liver Biopsy; Histological clusters: Cluster 3; Interface activity: None; Perivenular fibrosis: Mild; Ishak fibrosis stage: 1; Lobular inflammation: None; Portal inflammation: Mild Case marker detected.
Inflamed tissue Case GSM3333785 SAMPLE 21 Screening Visit_Cluster 2 Tissue: Liver Biopsy; Histological clusters: Cluster 2; Interface activity: None; Perivenular fibrosis: Moderate; Ishak fibrosis stage: 2; Lobular inflammation: None; Portal inflammation: Mild Case marker detected.
Inflamed tissue Case GSM3333786 SAMPLE 22 Screening Visit_Cluster 3 Tissue: Liver Biopsy; Histological clusters: Cluster 3; Interface activity: None; Perivenular fibrosis: Mild; Ishak fibrosis stage: 0; Lobular inflammation: None; Portal inflammation: None Case marker detected.
Inflamed tissue Case GSM3333787 SAMPLE 23 Screening Visit_Cluster 3 Tissue: Liver Biopsy; Histological clusters: Cluster 3; Interface activity: None; Perivenular fibrosis: None; Ishak fibrosis stage: 0; Lobular inflammation: None; Portal inflammation: Mild Case marker detected.
Inflamed tissue Case GSM3333788 SAMPLE 24 Screening Visit_Cluster 3 Tissue: Liver Biopsy; Histological clusters: Cluster 3; Interface activity: None; Perivenular fibrosis: Mild; Ishak fibrosis stage: 1; Lobular inflammation: None; Portal inflammation: None Case marker detected.
Inflamed tissue Case GSM3333789 SAMPLE 25 Screening Visit_Cluster 1 Tissue: Liver Biopsy; Histological clusters: Cluster 1; Interface activity: Mild; Perivenular fibrosis: Moderate; Ishak fibrosis stage: 3; Lobular inflammation: Mild; Portal inflammation: Mild Case marker detected.
Inflamed tissue Case GSM3333790 SAMPLE 26 Screening Visit_Cluster 2 Tissue: Liver Biopsy; Histological clusters: Cluster 2; Interface activity: None; Perivenular fibrosis: Moderate; Ishak fibrosis stage: 3; Lobular inflammation: None; Portal inflammation: Mild Case marker detected.
Inflamed tissue Case GSM3333791 SAMPLE 27 Screening Visit_Cluster 3 Tissue: Liver Biopsy; Histological clusters: Cluster 3; Interface activity: None; Perivenular fibrosis: Mild; Ishak fibrosis stage: 1; Lobular inflammation: None; Portal inflammation: Mild Case marker detected.
Inflamed tissue Case GSM3333792 SAMPLE 28 Screening Visit_Cluster 2 Tissue: Liver Biopsy; Histological clusters: Cluster 2; Interface activity: None; Perivenular fibrosis: Moderate; Ishak fibrosis stage: 3; Lobular inflammation: None; Portal inflammation: Mild Case marker detected.
Inflamed tissue Case GSM3333793 SAMPLE 29 Screening Visit_Cluster 2 Tissue: Liver Biopsy; Histological clusters: Cluster 2; Interface activity: None; Perivenular fibrosis: Mild; Ishak fibrosis stage: 2; Lobular inflammation: None; Portal inflammation: None Case marker detected.
Inflamed tissue Case GSM3333794 SAMPLE 30 Screening Visit_Cluster 2 Tissue: Liver Biopsy; Histological clusters: Cluster 2; Interface activity: None; Perivenular fibrosis: Moderate; Ishak fibrosis stage: 3; Lobular inflammation: Mild; Portal inflammation: Mild Case marker detected.
Inflamed tissue Case GSM3333795 SAMPLE 31 Screening Visit_Cluster 2 Tissue: Liver Biopsy; Histological clusters: Cluster 2; Interface activity: None; Perivenular fibrosis: Moderate; Ishak fibrosis stage: 3; Lobular inflammation: Mild; Portal inflammation: Mild Case marker detected.
Inflamed tissue Case GSM3333796 SAMPLE 32 Screening Visit_Cluster 3 Tissue: Liver Biopsy; Histological clusters: Cluster 3; Interface activity: None; Perivenular fibrosis: Mild; Ishak fibrosis stage: 1; Lobular inflammation: None; Portal inflammation: None Case marker detected.
Inflamed tissue Case GSM3333797 SAMPLE 33 Screening Visit_Cluster 1 Tissue: Liver Biopsy; Histological clusters: Cluster 1; Interface activity: Mild; Perivenular fibrosis: Mild; Ishak fibrosis stage: 3; Lobular inflammation: Mild; Portal inflammation: Mild Case marker detected.
Inflamed tissue Case GSM3333798 SAMPLE 34 Screening Visit_Cluster 3 Tissue: Liver Biopsy; Histological clusters: Cluster 3; Interface activity: None; Perivenular fibrosis: None; Ishak fibrosis stage: 1; Lobular inflammation: None; Portal inflammation: None Case marker detected.
Inflamed tissue Case GSM3333799 SAMPLE 35 Screening Visit_Cluster 3 Tissue: Liver Biopsy; Histological clusters: Cluster 3; Interface activity: None; Perivenular fibrosis: None; Ishak fibrosis stage: 0; Lobular inflammation: None; Portal inflammation: Mild Case marker detected.
Inflamed tissue Case GSM3333800 SAMPLE 36 Screening Visit_Cluster 2 Tissue: Liver Biopsy; Histological clusters: Cluster 2; Interface activity: None; Perivenular fibrosis: Moderate; Ishak fibrosis stage: 1; Lobular inflammation: None; Portal inflammation: None Case marker detected.
Inflamed tissue Case GSM3333801 SAMPLE 37 Screening Visit_Cluster 3 Tissue: Liver Biopsy; Histological clusters: Cluster 3; Interface activity: None; Perivenular fibrosis: Mild; Ishak fibrosis stage: 1; Lobular inflammation: None; Portal inflammation: None Case marker detected.
Inflamed tissue Case GSM3333802 SAMPLE 38 Screening Visit_Cluster 3 Tissue: Liver Biopsy; Histological clusters: Cluster 3; Interface activity: None; Perivenular fibrosis: Mild; Ishak fibrosis stage: 1; Lobular inflammation: None; Portal inflammation: None Case marker detected.
Inflamed tissue Case GSM3333803 SAMPLE 39 Screening Visit_Cluster 1 Tissue: Liver Biopsy; Histological clusters: Cluster 1; Interface activity: Mild; Perivenular fibrosis: Mild; Ishak fibrosis stage: 3; Lobular inflammation: Mild; Portal inflammation: Moderate Case marker detected.
Inflamed tissue Case GSM3333804 SAMPLE 40 Screening Visit_Cluster 2 Tissue: Liver Biopsy; Histological clusters: Cluster 2; Interface activity: None; Perivenular fibrosis: None; Ishak fibrosis stage: 3; Lobular inflammation: None; Portal inflammation: None Case marker detected.
Inflamed tissue Case GSM3333805 SAMPLE 41 Screening Visit_Cluster 3 Tissue: Liver Biopsy; Histological clusters: Cluster 3; Interface activity: None; Perivenular fibrosis: None; Ishak fibrosis stage: 1; Lobular inflammation: None; Portal inflammation: None Case marker detected.
Inflamed tissue Case GSM3333806 SAMPLE 42 Screening Visit_Cluster 3 Tissue: Liver Biopsy; Histological clusters: Cluster 3; Interface activity: None; Perivenular fibrosis: None; Ishak fibrosis stage: 0; Lobular inflammation: None; Portal inflammation: None Case marker detected.
Inflamed tissue Case GSM3333807 SAMPLE 43 Screening Visit_Cluster 2 Tissue: Liver Biopsy; Histological clusters: Cluster 2; Interface activity: None; Perivenular fibrosis: Moderate; Ishak fibrosis stage: 3; Lobular inflammation: Mild; Portal inflammation: Mild Case marker detected.
Inflamed tissue Case GSM3333808 SAMPLE 44 Screening Visit_Cluster 3 Tissue: Liver Biopsy; Histological clusters: Cluster 3; Interface activity: None; Perivenular fibrosis: None; Ishak fibrosis stage: 0; Lobular inflammation: None; Portal inflammation: Mild Case marker detected.
Inflamed tissue Case GSM3333809 SAMPLE 45 Screening Visit_Cluster 2 Tissue: Liver Biopsy; Histological clusters: Cluster 2; Interface activity: None; Perivenular fibrosis: Mild; Ishak fibrosis stage: 2; Lobular inflammation: None; Portal inflammation: Mild Case marker detected.
Inflamed tissue Case GSM3333810 SAMPLE 46 Screening Visit_Cluster 3 Tissue: Liver Biopsy; Histological clusters: Cluster 3; Interface activity: None; Perivenular fibrosis: Mild; Ishak fibrosis stage: 1; Lobular inflammation: Mild; Portal inflammation: None Case marker detected.
Inflamed tissue Case GSM3333811 SAMPLE 47 Screening Visit_Cluster 3 Tissue: Liver Biopsy; Histological clusters: Cluster 3; Interface activity: None; Perivenular fibrosis: None; Ishak fibrosis stage: 1; Lobular inflammation: Mild; Portal inflammation: None Case marker detected.
Inflamed tissue Case GSM3333812 SAMPLE 48 Screening Visit_Cluster 1 Tissue: Liver Biopsy; Histological clusters: Cluster 1; Interface activity: Mild; Perivenular fibrosis: Moderate; Ishak fibrosis stage: 1; Lobular inflammation: None; Portal inflammation: Mild Case marker detected.
Inflamed tissue Case GSM3333813 SAMPLE 49 Screening Visit_Cluster 2 Tissue: Liver Biopsy; Histological clusters: Cluster 2; Interface activity: None; Perivenular fibrosis: Moderate; Ishak fibrosis stage: 1; Lobular inflammation: None; Portal inflammation: None Case marker detected.
Inflamed tissue Case GSM3333814 SAMPLE 50 Screening Visit_Cluster 3 Tissue: Liver Biopsy; Histological clusters: Cluster 3; Interface activity: None; Perivenular fibrosis: None; Ishak fibrosis stage: 1; Lobular inflammation: None; Portal inflammation: None Case marker detected.
83 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.