GSE197112

Development of gene expression signatures for human 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

4 case / 4 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.

Source: GEO
Assay: microarray
Organism: Homo sapiens
Whole-study samples: 8 samples
Specimen: Biopsy
Reported/interpreted study design: Disease/model vs control Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Liu C, Le T
Contact name: Tao Le
Submission date: 2022-02-21
Last update: 2022-02-23
Organization: Shanghai University of traditional Chinese Medicine
Department: Department of Burns and Cutaneous Surgery, Xijing Hospital
Public date: 2022-02-22
Experiment types: Expression profiling by array; Non-coding RNA profiling by array
Platforms: GPL28576 OE Biotech Human ceRNA Microarray, Design ID:086188
Series type: Series
SubSeries: Not available
BioProject: PRJNA808997

Summary

To further development of our gene expression approach to biodosimetry, we have employed whole genome microarray expression profiling as a discovery platform to to study the genes that change in the progress of human liver fibrosis, so as to provide a basis for the clinical treatment of liver fibrosis.

Overall design

Gene expression was detected in 4 patients with liver fibrosis and 4 normal people

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 8 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 Related publications Biological aging accelerates hepatic fibrosis: Insights from the NHANES 2017-2020 and genome-wide association study analysis. Annals of hepatology, 2025 PubMed DOI Identifying the Crucial Biomarker of MASH-Related HCC. Combinatorial chemistry & high throughput screening, 2025 PubMed DOI	Available

Metadata Quality Components

Persisted metadata quality

100 pts

Clarity: 100%
Weight: 100 pts

Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Rule-based grouping found both case and control samples. 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: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.

Analysis Readiness

Review before analysis

97% DE readiness

Contrast completeness

25/25 pts

Both case and control groups are present in the proposed grouping.

Minimum group size

20/20 pts

Each contrast group has at least 2 samples.

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

7/10 pts

Warnings are present, but none are critical blockers.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

Secondary RNA assay context should be analyzed separately from ordinary bulk RNA-seq.

Next Steps

Review blockers and update sample grouping or dataset selection before analysis.

Analysis Preparation Checklist

5/6 ready

Group labels reviewed

Needs review

Siftome proposed case and control labels, but no reviewer confirmation is stored yet.

Open the sample grouping CSV and confirm group labels before analysis.

Minimum sample count met

Ready

Both groups meet the minimum of 2 samples.

Confirm whether the cohort is large enough for the intended statistical analysis.

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.

Assay context may require expert handling before DESeq2-style 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 4 samples
Likely control group Healthy control 4 samples

Intent Interpretation

Downgrade or exclusion reason Downgraded assay: microarray cohorts are separated from the RNA-seq intent. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

Comparison: Disease/model vs control. Specimen: Biopsy. Comparison suitability: 0%.
Interpreted disease metadata: Fibrosis, Liver fibrosis.
Processed data is available for downstream review.
External evidence: PubMed links 2 publications; 2 DOIs available: PMID 38726780, PMID 39426601.
Publication context: Identifying the Crucial Biomarker of MASH-Related HCC.. Combinatorial chemistry & high throughput screening, 2025. PMID 38726780. DOI 10.2174/0113862073287250240424073108.
Publication context: Biological aging accelerates hepatic fibrosis: Insights from the NHANES 2017-2020 and genome-wide association study analysis.. Annals of hepatology, 2025. PMID 39426601. DOI 10.1016/j.aohep.2024.101579.

Cautions

Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
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 fewer than ten samples limit cohort confidence.
Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
Microarray expression context was detected; compare separately from RNA-seq cohorts.
Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.

Normalized Fields

49 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source liver GSM5909318 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver tissue: liver sample-anatomical-source-v1 sample-local anatomical source

anatomical_source liver GSM5909319 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver tissue: liver sample-anatomical-source-v1 sample-local anatomical source

anatomical_source liver GSM5909320 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver tissue: liver sample-anatomical-source-v1 sample-local anatomical source

anatomical_source liver GSM5909321 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver tissue: liver sample-anatomical-source-v1 sample-local anatomical source

anatomical_source liver GSM5909322 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver tissue: liver sample-anatomical-source-v1 sample-local anatomical source

anatomical_source liver GSM5909323 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver tissue: liver sample-anatomical-source-v1 sample-local anatomical source

anatomical_source liver GSM5909324 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver tissue: liver sample-anatomical-source-v1 sample-local anatomical source

anatomical_source liver GSM5909325 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver tissue: liver sample-anatomical-source-v1 sample-local anatomical source

assay_type microarray GSE197112 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence microarray dataset_accession: GSE197112 dataset_title: Development of gene expression signatures for human liver fibrosis organism: Homo sapiens assay_type: microarray processed_data_avail... keyword match keyword match: microarray

collection_method biopsy GSM5909318 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy fibrosis1 liver fibrosis people biopsy tissue1 disease state: liver fibrosis; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM5909319 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy fibrosis2 liver fibrosis people biopsy tissue2 disease state: liver fibrosis; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM5909320 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy fibrosis3 liver fibrosis people biopsy tissue3 disease state: liver fibrosis; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM5909321 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy fibrosis4 liver fibrosis people biopsy tissue4 disease state: liver fibrosis; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM5909322 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy non-fibrosis1 normal people liver biopsy tissue1 disease state: normal; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM5909323 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy non-fibrosis2 normal people liver biopsy tissue2 disease state: normal; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM5909324 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy non-fibrosis3 normal people liver biopsy tissue3 disease state: normal; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM5909325 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy non-fibrosis4 normal people liver biopsy tissue4 disease state: normal; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary collection method match: biopsy

disease fibrosis GSE197112 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence fibrosis dataset_accession: GSE197112 dataset_title: Development of gene expression signatures for human liver fibrosis organism: Homo sapiens assay_type: microarray processed_data_avail... controlled vocabulary controlled vocabulary disease match: fibrosis

disease liver fibrosis GSE197112 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver fibrosis dataset_accession: GSE197112 dataset_title: Development of gene expression signatures for human liver fibrosis organism: Homo sapiens assay_type: microarray processed_data_avail... controlled vocabulary controlled vocabulary disease match: liver fibrosis

disease fibrosis GSM5909318 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence fibrosis fibrosis1 liver fibrosis people biopsy tissue1 disease state: liver fibrosis; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary disease match: fibrosis

disease liver fibrosis GSM5909318 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver fibrosis fibrosis1 liver fibrosis people biopsy tissue1 disease state: liver fibrosis; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary disease match: liver fibrosis

disease fibrosis GSM5909319 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence fibrosis fibrosis2 liver fibrosis people biopsy tissue2 disease state: liver fibrosis; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary disease match: fibrosis

disease liver fibrosis GSM5909319 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver fibrosis fibrosis2 liver fibrosis people biopsy tissue2 disease state: liver fibrosis; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary disease match: liver fibrosis

disease fibrosis GSM5909320 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence fibrosis fibrosis3 liver fibrosis people biopsy tissue3 disease state: liver fibrosis; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary disease match: fibrosis

disease liver fibrosis GSM5909320 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver fibrosis fibrosis3 liver fibrosis people biopsy tissue3 disease state: liver fibrosis; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary disease match: liver fibrosis

disease fibrosis GSM5909321 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence fibrosis fibrosis4 liver fibrosis people biopsy tissue4 disease state: liver fibrosis; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary disease match: fibrosis

disease liver fibrosis GSM5909321 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver fibrosis fibrosis4 liver fibrosis people biopsy tissue4 disease state: liver fibrosis; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary disease match: liver fibrosis

organism Homo sapiens GSE197112 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE197112 dataset_title: Development of gene expression signatures for human liver fibrosis organism: Homo sapiens assay_type: microarray processed_data_avail... keyword match keyword match: homo sapiens

primary_tissue primary tissue GSM5909318 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy fibrosis1 liver fibrosis people biopsy tissue1 disease state: liver fibrosis; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM5909319 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy fibrosis2 liver fibrosis people biopsy tissue2 disease state: liver fibrosis; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM5909320 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy fibrosis3 liver fibrosis people biopsy tissue3 disease state: liver fibrosis; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM5909321 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy fibrosis4 liver fibrosis people biopsy tissue4 disease state: liver fibrosis; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM5909322 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy non-fibrosis1 normal people liver biopsy tissue1 disease state: normal; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM5909323 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy non-fibrosis2 normal people liver biopsy tissue2 disease state: normal; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM5909324 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy non-fibrosis3 normal people liver biopsy tissue3 disease state: normal; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM5909325 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy non-fibrosis4 normal people liver biopsy tissue4 disease state: normal; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary primary tissue match: biopsy

sample_type normal tissue GSM5909322 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal non-fibrosis1 normal people liver biopsy tissue1 disease state: normal; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM5909323 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal non-fibrosis2 normal people liver biopsy tissue2 disease state: normal; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM5909324 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal non-fibrosis3 normal people liver biopsy tissue3 disease state: normal; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM5909325 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal non-fibrosis4 normal people liver biopsy tissue4 disease state: normal; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary sample type match: normal

tissue liver GSE197112 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver dataset_accession: GSE197112 dataset_title: Development of gene expression signatures for human liver fibrosis organism: Homo sapiens assay_type: microarray processed_data_avail... controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM5909318 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver fibrosis1 liver fibrosis people biopsy tissue1 disease state: liver fibrosis; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM5909319 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver fibrosis2 liver fibrosis people biopsy tissue2 disease state: liver fibrosis; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM5909320 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver fibrosis3 liver fibrosis people biopsy tissue3 disease state: liver fibrosis; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM5909321 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver fibrosis4 liver fibrosis people biopsy tissue4 disease state: liver fibrosis; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM5909322 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver non-fibrosis1 normal people liver biopsy tissue1 disease state: normal; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM5909323 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver non-fibrosis2 normal people liver biopsy tissue2 disease state: normal; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM5909324 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver non-fibrosis3 normal people liver biopsy tissue3 disease state: normal; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM5909325 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver non-fibrosis4 normal people liver biopsy tissue4 disease state: normal; tissue: liver; Sex: pooled male and female controlled vocabulary controlled vocabulary tissue match: liver

Sample Group Preview

8 rows shown Show Hide

Study totals: Case 4 | Control 4 | Unassigned 0 | Excluded 0 | Ambiguous 0 8 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Liver fibrosis	Case	GSM5909318	Fibrosis1	Liver fibrosis people biopsy tissue1 Disease state: Liver fibrosis; Tissue: Liver; Sex: Pooled male and female	Case marker detected.
Liver fibrosis	Case	GSM5909319	Fibrosis2	Liver fibrosis people biopsy tissue2 Disease state: Liver fibrosis; Tissue: Liver; Sex: Pooled male and female	Case marker detected.
Liver fibrosis	Case	GSM5909320	Fibrosis3	Liver fibrosis people biopsy tissue3 Disease state: Liver fibrosis; Tissue: Liver; Sex: Pooled male and female	Case marker detected.
Liver fibrosis	Case	GSM5909321	Fibrosis4	Liver fibrosis people biopsy tissue4 Disease state: Liver fibrosis; Tissue: Liver; Sex: Pooled male and female	Case marker detected.
Healthy control	Control	GSM5909322	Non-fibrosis1	Normal people liver biopsy tissue1 Disease state: Normal; Tissue: Liver; Sex: Pooled male and female	Sample-local control marker detected.
Healthy control	Control	GSM5909323	Non-fibrosis2	Normal people liver biopsy tissue2 Disease state: Normal; Tissue: Liver; Sex: Pooled male and female	Sample-local control marker detected.
Healthy control	Control	GSM5909324	Non-fibrosis3	Normal people liver biopsy tissue3 Disease state: Normal; Tissue: Liver; Sex: Pooled male and female	Sample-local control marker detected.
Healthy control	Control	GSM5909325	Non-fibrosis4	Normal people liver biopsy tissue4 Disease state: Normal; Tissue: Liver; Sex: Pooled male and female	Sample-local control 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.

Summary

Overall design

Source Evidence

Related publications

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