GSE171294

The next-generation sequencing was helpful for the quantitative analysis of the normal control group and the liver fibrosis group

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: bulk RNA-seq
Organism: Homo sapiens
Whole-study samples: 8 samples
Specimen: Tissue
Reported/interpreted study design: Disease/model vs control Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Ni X, Peng S, Fu L, Wu C, Cichun W
Contact name: Wu Cichun
Submission date: 2021-04-01
Last update: 2021-08-03
Organization: Cichunwu
Department: Not available
Public date: 2021-08-03
Experiment types: Expression profiling by high throughput sequencing
Platforms: GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Series type: Series
SubSeries: Not available
BioProject: PRJNA719144

Summary

Ten snap-frozen liver tissues were used for RNA sequencing (RNA-seq) and were obtained from 8 patients who underwent surgical resection for the treatment of HBV-associated liver cancer in the liver fibrosis group (n=4) or hemangioma in the control group (n=4). RNA-seq showed that 1246 genes were aberrantly expressed with more than log2-fold change in liver fibrosis tissues than in normal control tissues (P<0.05). Among these, 687 genes were significantly up-regulated and 559 genes were down-regulated.

Overall design

Normal liver tissue and liver fibrosis patients.

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. 4 linked publications 4 DOIs Primary publication Hepatic BRD4 Is Upregulated in Liver Fibrosis of Various Etiologies and Positively Correlated to Fibrotic Severity. Frontiers in medicine, 2021 PubMed DOI Related publications RAB25 promotes hepatitis B virus-induced liver fibrosis progression through activation of the PI3K/AKT signaling pathway. Virus research, 2026 PubMed DOI Comparative molecular analysis of oral submucous fibrosis and other organ fibrosis based on weighted gene co-expression network analysis. Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences, 2022 PubMed DOI Exploration of new therapeutic targets for viral hepatic fibrosis, alcoholic hepatic fibrosis, and non-alcoholic hepatic fibrosis. Annals of translational medicine, 2022 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

Ready after review

100% 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

10/10 pts

No dataset warnings are present.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

No readiness blockers detected.

Next Steps

Verify the proposed sample assignments and case-versus-control comparison against the GEO metadata before using them in DESeq2 or another differential-expression tool.
Confirm processed count files and sample identifiers match the exported metadata.

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

Standard analyst review

Proceed only after the analyst confirms grouping, exclusions, and source files.

By Siftome standards, no expert review was triggered.

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 Fibrosis, liver cancer, liver fibrosis Disease context came from Normalization rules.
Likely case group Liver fibrosis 4 samples
Likely control group Healthy control 4 samples

Ranking Facts

Supporting evidence

Comparison: Disease/model vs control. Specimen: Tissue. Comparison suitability: 0%.
Prioritized assay: bulk RNA-seq is the active assay expectation.
Interpreted disease metadata: Fibrosis, Liver cancer, Liver fibrosis.
Processed data is available for downstream review.
External evidence: PubMed links 4 publications; 4 DOIs available: PMID 34336890, PMID 36111046, PMID 36748376, PMID 41651076.
Publication context: Hepatic BRD4 Is Upregulated in Liver Fibrosis of Various Etiologies and Positively Correlated to Fibrotic Severity.. Frontiers in medicine, 2021. PMID 34336890. DOI 10.3389/fmed.2021.683506.
Publication context: Exploration of new therapeutic targets for viral hepatic fibrosis, alcoholic hepatic fibrosis, and non-alcoholic hepatic fibrosis.. Annals of translational medicine, 2022. PMID 36111046. DOI 10.21037/atm-22-3593.
Publication context: Comparative molecular analysis of oral submucous fibrosis and other organ fibrosis based on weighted gene co-expression network analysis.. Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences, 2022. PMID 36748376. DOI 10.11817/j.issn.1672-7347.2022.220452.
Publication context: 1 additional linked PubMed publications are available.

Cautions

Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
Overall score capped because comparison suitability is weak for the selected search intent.
Overall score capped because fewer than ten samples limit cohort confidence.
Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

No dataset warnings

Normalized Fields

38 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source liver GSM5222239 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver tissue: Liver sample-anatomical-source-v1 sample-local anatomical source

anatomical_source liver GSM5222240 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver tissue: Liver sample-anatomical-source-v1 sample-local anatomical source

anatomical_source liver GSM5222241 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver tissue: Liver sample-anatomical-source-v1 sample-local anatomical source

anatomical_source liver GSM5222242 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver tissue: Liver sample-anatomical-source-v1 sample-local anatomical source

anatomical_source liver GSM5222243 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver tissue: Liver sample-anatomical-source-v1 sample-local anatomical source

anatomical_source liver GSM5222244 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver tissue: Liver sample-anatomical-source-v1 sample-local anatomical source

anatomical_source liver GSM5222245 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver tissue: Liver sample-anatomical-source-v1 sample-local anatomical source

anatomical_source liver GSM5222246 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver tissue: Liver sample-anatomical-source-v1 sample-local anatomical source

assay_type bulk RNA-seq GSE171294 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence bulk rna-seq dataset_accession: GSE171294 dataset_title: The next-generation sequencing was helpful for the quantitative analysis of the normal control group and the liver fibrosis group org... keyword match keyword match: bulk rna-seq

control_type healthy control GSM5222239 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence normal control NC1 Liver tissue: Liver; group: Normal control controlled vocabulary controlled vocabulary control type match: normal control

control_type healthy control GSM5222240 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence normal control NC2 Liver tissue: Liver; group: Normal control controlled vocabulary controlled vocabulary control type match: normal control

control_type healthy control GSM5222241 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence normal control NC3 Liver tissue: Liver; group: Normal control controlled vocabulary controlled vocabulary control type match: normal control

control_type healthy control GSM5222242 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence normal control NC4 Liver tissue: Liver; group: Normal control controlled vocabulary controlled vocabulary control type match: normal control

disease fibrosis GSE171294 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence fibrosis dataset_accession: GSE171294 dataset_title: The next-generation sequencing was helpful for the quantitative analysis of the normal control group and the liver fibrosis group org... controlled vocabulary controlled vocabulary disease match: fibrosis

disease liver cancer GSE171294 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver cancer dataset_accession: GSE171294 dataset_title: The next-generation sequencing was helpful for the quantitative analysis of the normal control group and the liver fibrosis group org... controlled vocabulary controlled vocabulary disease match: liver cancer

disease liver fibrosis GSE171294 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver fibrosis dataset_accession: GSE171294 dataset_title: The next-generation sequencing was helpful for the quantitative analysis of the normal control group and the liver fibrosis group org... controlled vocabulary controlled vocabulary disease match: liver fibrosis

disease fibrosis GSM5222243 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence fibrosis LF1 Liver tissue: Liver; group: Liver fibrosis controlled vocabulary controlled vocabulary disease match: fibrosis

disease liver fibrosis GSM5222243 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver fibrosis LF1 Liver tissue: Liver; group: Liver fibrosis controlled vocabulary controlled vocabulary disease match: liver fibrosis

disease fibrosis GSM5222244 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence fibrosis LF2 Liver tissue: Liver; group: Liver fibrosis controlled vocabulary controlled vocabulary disease match: fibrosis

disease liver fibrosis GSM5222244 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver fibrosis LF2 Liver tissue: Liver; group: Liver fibrosis controlled vocabulary controlled vocabulary disease match: liver fibrosis

disease fibrosis GSM5222245 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence fibrosis LF3 Liver tissue: Liver; group: Liver fibrosis controlled vocabulary controlled vocabulary disease match: fibrosis

disease liver fibrosis GSM5222245 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver fibrosis LF3 Liver tissue: Liver; group: Liver fibrosis controlled vocabulary controlled vocabulary disease match: liver fibrosis

disease fibrosis GSM5222246 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence fibrosis LF4 Liver tissue: Liver; group: Liver fibrosis controlled vocabulary controlled vocabulary disease match: fibrosis

disease liver fibrosis GSM5222246 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence liver fibrosis LF4 Liver tissue: Liver; group: Liver fibrosis controlled vocabulary controlled vocabulary disease match: liver fibrosis

organism Homo sapiens GSE171294 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE171294 dataset_title: The next-generation sequencing was helpful for the quantitative analysis of the normal control group and the liver fibrosis group org... keyword match keyword match: homo sapiens

sample_type normal tissue GSM5222239 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal NC1 Liver tissue: Liver; group: Normal control controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM5222240 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal NC2 Liver tissue: Liver; group: Normal control controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM5222241 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal NC3 Liver tissue: Liver; group: Normal control controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM5222242 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal NC4 Liver tissue: Liver; group: Normal control controlled vocabulary controlled vocabulary sample type match: normal

tissue liver GSE171294 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver dataset_accession: GSE171294 dataset_title: The next-generation sequencing was helpful for the quantitative analysis of the normal control group and the liver fibrosis group org... controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM5222239 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver NC1 Liver tissue: Liver; group: Normal control controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM5222240 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver NC2 Liver tissue: Liver; group: Normal control controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM5222241 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver NC3 Liver tissue: Liver; group: Normal control controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM5222242 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver NC4 Liver tissue: Liver; group: Normal control controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM5222243 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver LF1 Liver tissue: Liver; group: Liver fibrosis controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM5222244 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver LF2 Liver tissue: Liver; group: Liver fibrosis controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM5222245 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver LF3 Liver tissue: Liver; group: Liver fibrosis controlled vocabulary controlled vocabulary tissue match: liver

tissue liver GSM5222246 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence liver LF4 Liver tissue: Liver; group: Liver fibrosis 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	GSM5222243	LF1	Liver Tissue: Liver; Group: Liver fibrosis	Case marker detected.
Liver fibrosis	Case	GSM5222244	LF2	Liver Tissue: Liver; Group: Liver fibrosis	Case marker detected.
Liver fibrosis	Case	GSM5222245	LF3	Liver Tissue: Liver; Group: Liver fibrosis	Case marker detected.
Liver fibrosis	Case	GSM5222246	LF4	Liver Tissue: Liver; Group: Liver fibrosis	Case marker detected.
Healthy control	Control	GSM5222239	NC1	Liver Tissue: Liver; Group: Normal control	Sample-local control marker detected.
Healthy control	Control	GSM5222240	NC2	Liver Tissue: Liver; Group: Normal control	Sample-local control marker detected.
Healthy control	Control	GSM5222241	NC3	Liver Tissue: Liver; Group: Normal control	Sample-local control marker detected.
Healthy control	Control	GSM5222242	NC4	Liver Tissue: Liver; Group: Normal control	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

Primary publication

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

Ranking Facts

Supporting evidence

Cautions

Dataset Warnings

Normalized Fields

Sample Group Preview

Use as Discovery Cohort