GSE7741

Expression data of HCV-associated advance disease state

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

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.

Source: GEO
Assay: microarray
Organism: Homo sapiens
Whole-study samples: 3 samples
Specimen: Biopsy
Reported/interpreted study design: Unclear study design Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Sarfraz S, Hamid S, Siddiqui A, Lee C, Qureshi A, Qureshi N, Khalid S
Contact name: Saira Khalid
Submission date: 2007-05-05
Last update: 2019-12-18
Organization: King Saud University
Department: Not available
Public date: 2007-11-01
Experiment types: Expression profiling by array
Platforms: GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
Series type: Series
SubSeries: Not available
BioProject: PRJNA99851

Summary

Introduction: Mechanisms that contribute to the pathogenesis of liver damage caused by hepatitis C virus (HCV) are not fully understood. Our previous work on liver biopsies from chronic HCV patients has shown modulation of the expression of certain cell cycle proteins indicating HCV-induced modifications of cell cycle events. We therefore hypothesize that HCV infection disrupts normal regulation of cell cycle that contributes to disease progression. Objective: To identify molecular disruptions during the course of HCV-associated disease progression, using liver biopsy specimens of chronic hepatitis C patients. Methods: Liver biopsy samples classified on histological basis as early (fibrosis stage 0-1) or advanced (fibrosis stage 3-4) disease stage were studied using oligonucleotide array ( HG U133 Plus 2.0, Affymetrix GeneChip™ System). For comparison, liver specimens from patients with non-viral hepatitis were also analyzed by microarray. Expression data was analyzed using Genespring (GX 7.2) and Ingenuity Pathway analysis (3.0). The differential expression of selected cell cycle genes (cyclin D2, KPNA2, HERC5 and Bcl-2) identified after microarray analysis was confirmed by quantitative real-time RT-PCR. Results: Microarray analysis revealed two-fold or greater transcriptional change in 792 genes of the total 38,500 known human genes in HCV-advance disease stage (HCV-A) as compared to HCV-early disease stage (HCV-E). Most of the genes have a defined role in immune response, extracellular matrix and cell cycle and apoptosis. Keywords: HCV-advance disease state

Overall design

Liver biopsy samples were collected from patients of (a) HCV-infected early disease stage (HCV-E, control 1) (b) non-HCV advance disease stage (control 2) and (c) HCV-infected advance disease stage (HCV-A) for RNA extraction. Equal amount of RNA was pooled from samples (n=4)within each group and hybridized to HG-U133 Plus 2.0 array.

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 3 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 Gene profiling of early and advanced liver disease in chronic hepatitis C patients. Hepatology international, 2011 PubMed DOI	Available

Metadata Quality Components

Persisted metadata quality

75 pts

Clarity: 75%
Weight: 100 pts

Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Case and control groups are not clear from sample metadata. Disease clarity: Disease or condition metadata normalized. Tissue clarity: Anatomical source metadata normalized. Treatment clarity: No unclear treatment split detected in the sample metadata. Replicate clarity: Pooled samples or technical replicates need review before trusting group counts. Data availability clarity: Dataset-level processed or raw data availability is explicit.

Analysis Readiness

Not ready

39% DE readiness

Contrast completeness

0/25 pts

No usable case/control contrast was detected.

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

12/15 pts

All non-excluded samples are assigned; excluded samples should still be confirmed.

Blocking warnings

0/10 pts

Critical warnings must be resolved before downstream analysis.

Metadata normalization

7/10 pts

Metadata quality is usable, but still deserves review.

Blockers

No complete case/control contrast is available.
Critical dataset warnings must be resolved.

Next Steps

Confirm excluded samples before creating the final analysis metadata file.
Resolve critical warnings before downstream analysis.

Analysis Preparation Checklist

3/6 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

Needs review

3 samples have hard exclusion flags in the proposed grouping.

Confirm excluded samples and preserve the reason in the analysis handoff.

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 No case group detected 0 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, Infectious disease or host response, Liver fibrosis.
Processed data is available for downstream review.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 21484131.
Publication context: Gene profiling of early and advanced liver disease in chronic hepatitis C patients.. Hepatology international, 2011. PMID 21484131. DOI 10.1007/s12072-011-9252-4.

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.
Pooled or technical replicate samples reduce suitability.
Missing or unclear metadata. Group clarity - Case and control groups are not clear from sample metadata.
Overall score capped because comparison suitability is weak for the selected search intent.
Overall score capped because fewer than six samples are too small for top-ranked cohort confidence.
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

No clear control group was detected from normalized metadata.
Pooled samples were detected and may need exclusion.
Total sample count is below the minimum needed for two comparison groups.
Microarray expression context was detected; compare separately from RNA-seq cohorts.
Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.
Patient-tissue tumor-normal intent requires clear tumor-normal grouping.

Normalized Fields

24 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source liver GSM182149 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver Tissue: Liver biopsy tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source liver GSM182150 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver Tissue: Liver biopsy tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source liver GSM182151 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver Tissue: Liver tissues sample-anatomical-source-v1 sample-local anatomical source

assay_type microarray GSE7741 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence microarray dataset_accession: GSE7741 dataset_title: Expression data of HCV-associated advance disease state organism: Homo sapiens assay_type: microarray processed_data_available: true ra... keyword match keyword match: microarray

collection_method biopsy GSM182149 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy HCV infected liver _Fibrosis Stage 0_pool1 Pooled early fibrosis Stage 0 of chronic HCV infected liver Tissue: Liver biopsy tissue; Disease stage: A pooled RNA sample from 4 liv... controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM182150 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Non-viral hepatic liver_pool1 Pooled Non-viral hepatitis Tissue: Liver biopsy tissue; Disease state: A pooled RNA sample from 3 liver tissues with non-viral hepatitis fibrosis s... controlled vocabulary controlled vocabulary collection method match: biopsy

disease fibrosis GSE7741 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence fibrosis dataset_accession: GSE7741 dataset_title: Expression data of HCV-associated advance disease state organism: Homo sapiens assay_type: microarray processed_data_available: true ra... controlled vocabulary controlled vocabulary disease match: fibrosis

disease liver fibrosis GSE7741 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence fibrosis stage dataset_accession: GSE7741 dataset_title: Expression data of HCV-associated advance disease state organism: Homo sapiens assay_type: microarray processed_data_available: true ra... controlled vocabulary controlled vocabulary disease match: fibrosis stage

disease fibrosis GSM182149 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence fibrosis HCV infected liver _Fibrosis Stage 0_pool1 Pooled early fibrosis Stage 0 of chronic HCV infected liver Tissue: Liver biopsy tissue; Disease stage: A pooled RNA sample from 4 liv... controlled vocabulary controlled vocabulary disease match: fibrosis

disease liver fibrosis GSM182149 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver fibrosis HCV infected liver _Fibrosis Stage 0_pool1 Pooled early fibrosis Stage 0 of chronic HCV infected liver Tissue: Liver biopsy tissue; Disease stage: A pooled RNA sample from 4 liv... controlled vocabulary controlled vocabulary disease match: liver fibrosis

disease fibrosis GSM182150 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence fibrosis Non-viral hepatic liver_pool1 Pooled Non-viral hepatitis Tissue: Liver biopsy tissue; Disease state: A pooled RNA sample from 3 liver tissues with non-viral hepatitis fibrosis s... controlled vocabulary controlled vocabulary disease match: fibrosis

disease liver fibrosis GSM182150 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence fibrosis stage Non-viral hepatic liver_pool1 Pooled Non-viral hepatitis Tissue: Liver biopsy tissue; Disease state: A pooled RNA sample from 3 liver tissues with non-viral hepatitis fibrosis s... controlled vocabulary controlled vocabulary disease match: fibrosis stage

disease fibrosis GSM182151 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence fibrosis HCV infected liver_Advance Fibrosis pool Pooled advance fibrosis stage III-IV chronic HCV infected liver Tissue: Liver tissues; Disease state: A pooled RNA sample from 4 liver t... controlled vocabulary controlled vocabulary disease match: fibrosis

disease liver fibrosis GSM182151 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence fibrosis stage HCV infected liver_Advance Fibrosis pool Pooled advance fibrosis stage III-IV chronic HCV infected liver Tissue: Liver tissues; Disease state: A pooled RNA sample from 4 liver t... controlled vocabulary controlled vocabulary disease match: fibrosis stage

organism Homo sapiens GSE7741 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE7741 dataset_title: Expression data of HCV-associated advance disease state organism: Homo sapiens assay_type: microarray processed_data_available: true ra... keyword match keyword match: homo sapiens

primary_tissue primary tissue GSM182149 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy HCV infected liver _Fibrosis Stage 0_pool1 Pooled early fibrosis Stage 0 of chronic HCV infected liver Tissue: Liver biopsy tissue; Disease stage: A pooled RNA sample from 4 liv... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM182150 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Non-viral hepatic liver_pool1 Pooled Non-viral hepatitis Tissue: Liver biopsy tissue; Disease state: A pooled RNA sample from 3 liver tissues with non-viral hepatitis fibrosis s... controlled vocabulary controlled vocabulary primary tissue match: biopsy

sample_type inflamed tissue GSM182149 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflammation HCV infected liver _Fibrosis Stage 0_pool1 Pooled early fibrosis Stage 0 of chronic HCV infected liver Tissue: Liver biopsy tissue; Disease stage: A pooled RNA sample from 4 liv... controlled vocabulary controlled vocabulary sample type match: inflammation

sample_type inflamed tissue GSM182150 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflammation Non-viral hepatic liver_pool1 Pooled Non-viral hepatitis Tissue: Liver biopsy tissue; Disease state: A pooled RNA sample from 3 liver tissues with non-viral hepatitis fibrosis s... controlled vocabulary controlled vocabulary sample type match: inflammation

sample_type inflamed tissue GSM182151 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflammation HCV infected liver_Advance Fibrosis pool Pooled advance fibrosis stage III-IV chronic HCV infected liver Tissue: Liver tissues; Disease state: A pooled RNA sample from 4 liver t... controlled vocabulary controlled vocabulary sample type match: inflammation

tissue liver GSE7741 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver dataset_accession: GSE7741 dataset_title: Expression data of HCV-associated advance disease state organism: Homo sapiens assay_type: microarray processed_data_available: true ra... controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM182149 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver HCV infected liver _Fibrosis Stage 0_pool1 Pooled early fibrosis Stage 0 of chronic HCV infected liver Tissue: Liver biopsy tissue; Disease stage: A pooled RNA sample from 4 liv... controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM182150 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver Non-viral hepatic liver_pool1 Pooled Non-viral hepatitis Tissue: Liver biopsy tissue; Disease state: A pooled RNA sample from 3 liver tissues with non-viral hepatitis fibrosis s... controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM182151 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver HCV infected liver_Advance Fibrosis pool Pooled advance fibrosis stage III-IV chronic HCV infected liver Tissue: Liver tissues; Disease state: A pooled RNA sample from 4 liver t... controlled vocabulary controlled vocabulary tissue match: liver

Sample Group Preview

3 rows shown Show Hide

Study totals: Case 0 | Control 0 | Unassigned 0 | Excluded 3 | Ambiguous 0 3 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Excluded: Pooled sample	Excluded	GSM182149	HCV infected liver _Fibrosis Stage 0_pool1	Pooled early fibrosis Stage 0 of chronic HCV infected liver Tissue: Liver biopsy tissue; Disease stage: A pooled RNA sample from 4 liver tissues with chronic hepatitis C, fibrosis stage 0, grade of inflammation 0-1.	pooled sample: Pooled sample metadata detected.
Excluded: Pooled sample	Excluded	GSM182150	Non-viral hepatic liver_pool1	Pooled Non-viral hepatitis Tissue: Liver biopsy tissue; Disease state: A pooled RNA sample from 3 liver tissues with non-viral hepatitis fibrosis stage 3, grade of inflammation II; Male to female ratio: 1/2	pooled sample: Pooled sample metadata detected.
Excluded: Pooled sample	Excluded	GSM182151	HCV infected liver_Advance Fibrosis pool	Pooled advance fibrosis stage III-IV chronic HCV infected liver Tissue: Liver tissues; Disease state: A pooled RNA sample from 4 liver tissues with chronic hepatitis C fibrosis stage III and IV, grade of inflammation III-IV; Male to female ratio: 1/3	pooled sample: Pooled sample metadata 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.

Summary

Overall design

Source Evidence

Primary publication

Metadata Quality Components

Analysis Readiness

Blockers

Next Steps

Analysis Preparation Checklist

Bioinformatician Review

Why This Is Ranked Here

Applied Review Decisions

Derived Classifications

Intent Interpretation

Ranking Facts

Supporting evidence

Cautions

Dataset Warnings

Normalized Fields

Sample Group Preview

Use as Discovery Cohort