GSE134025

Ulcerative colitis gene expressions file

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

3 case / 3 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: 6 samples
Specimen: Tissue
Reported/interpreted study design: Disease/model vs control Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Tao J
Contact name: Jin Tao
Submission date: 2019-07-09
Last update: 2020-02-10
Organization: The Third Affiliated Hospital of Sun Yat-Sen University
Department: Department of Gastroenterology
Public date: 2019-07-10
Experiment types: Expression profiling by array
Platforms: GPL20115 Agilent-067406 Human CBC lncRNA + mRNA microarray V4.0 (Probe name version)
Series type: Series
SubSeries: Not available
BioProject: PRJNA553508

Summary

Ulcerative colitis related gene expressions analysis in colonic biopsy samples from control and ulcerative colitis patients

Overall design

Three paired colonic mucosal samples from colitis patients and control individuals were collected. Total RNA of each one was extracted and reverse transcribed into cDNA. The cDNA then processed for gene expression microanalysis.

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 6 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 3 DOIs Primary publication Ferroptosis involves in intestinal epithelial cell death in ulcerative colitis. Cell death & disease, 2020 PubMed DOI Related publications Gancao Xiexin decoction attenuated experimental colitis through suppressing ACSL4-mediated ferroptosis. Journal of ethnopharmacology, 2025 PubMed DOI Identification of Pharmacological Autophagy Regulators of Active Ulcerative Colitis. Frontiers in pharmacology, 2021 PubMed DOI [Bioinformatic analysis of molecular mechanism of IL-17 in regulating ulcerative colitis]. Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology, 2023 PubMed	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

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

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

Bioinformatician review required

Ask a bioinformatician to review grouping, count availability, exclusions, and design 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 Ulcerative colitis Disease context came from Normalization rules.
Likely case group Ulcerative colitis 3 samples
Likely control group Healthy control 3 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: Tissue. Comparison suitability: 0%.
Interpreted disease metadata: Ulcerative colitis.
Processed data is available for downstream review.
External evidence: PubMed links 4 publications; 3 DOIs available: PMID 32015337, PMID 34925026, PMID 36631011, PMID 39993549.
Publication context: Ferroptosis involves in intestinal epithelial cell death in ulcerative colitis.. Cell death & disease, 2020. PMID 32015337. DOI 10.1038/s41419-020-2299-1.
Publication context: Identification of Pharmacological Autophagy Regulators of Active Ulcerative Colitis.. Frontiers in pharmacology, 2021. PMID 34925026. DOI 10.3389/fphar.2021.769718.
Publication context: [Bioinformatic analysis of molecular mechanism of IL-17 in regulating ulcerative colitis].. Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology, 2023. PMID 36631011.
Publication context: 1 additional linked PubMed publications are available.

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.
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

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

34 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source colon GSM3933487 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colonic tissue: colonic mucosa sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM3933487 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colonic mucosa tissue: colonic mucosa sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM3933488 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colonic tissue: colonic mucosa sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM3933488 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colonic mucosa tissue: colonic mucosa sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM3933489 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colonic tissue: colonic mucosa sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM3933489 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colonic mucosa tissue: colonic mucosa sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM3933490 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colonic tissue: colonic mucosa sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM3933490 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colonic mucosa tissue: colonic mucosa sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM3933491 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colonic tissue: colonic mucosa sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM3933491 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colonic mucosa tissue: colonic mucosa sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM3933492 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colonic tissue: colonic mucosa sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM3933492 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colonic mucosa tissue: colonic mucosa sample-anatomical-source-v1 sample-local anatomical source

assay_type microarray GSE134025 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence microarray dataset_accession: GSE134025 dataset_title: Ulcerative colitis gene expressions file organism: Homo sapiens assay_type: microarray processed_data_available: true raw_data_availa... keyword match keyword match: microarray

control_type healthy control GSM3933490 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control Normal 1 colonic mucosal sample tissue: colonic mucosa; diagnosis: healthy control controlled vocabulary controlled vocabulary control type match: healthy control

control_type healthy control GSM3933491 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control Normal 2 colonic mucosal sample tissue: colonic mucosa; diagnosis: healthy control controlled vocabulary controlled vocabulary control type match: healthy control

control_type healthy control GSM3933492 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control Normal 3 colonic mucosal sample tissue: colonic mucosa; diagnosis: healthy control controlled vocabulary controlled vocabulary control type match: healthy control

disease ulcerative colitis GSE134025 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis dataset_accession: GSE134025 dataset_title: Ulcerative colitis gene expressions file organism: Homo sapiens assay_type: microarray processed_data_available: true raw_data_availa... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM3933487 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis UC patient 1 colonic mucosal sample tissue: colonic mucosa; diagnosis: ulcerative colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM3933488 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis UC patient 2 colonic mucosal sample tissue: colonic mucosa; diagnosis: ulcerative colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM3933489 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis UC patient 3 colonic mucosal sample tissue: colonic mucosa; diagnosis: ulcerative colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

normal_tissue_type healthy donor tissue GSM3933490 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control Normal 1 colonic mucosal sample tissue: colonic mucosa; diagnosis: healthy control controlled vocabulary controlled vocabulary normal tissue type match: healthy control

normal_tissue_type healthy donor tissue GSM3933491 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control Normal 2 colonic mucosal sample tissue: colonic mucosa; diagnosis: healthy control controlled vocabulary controlled vocabulary normal tissue type match: healthy control

normal_tissue_type healthy donor tissue GSM3933492 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control Normal 3 colonic mucosal sample tissue: colonic mucosa; diagnosis: healthy control controlled vocabulary controlled vocabulary normal tissue type match: healthy control

organism Homo sapiens GSE134025 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE134025 dataset_title: Ulcerative colitis gene expressions file organism: Homo sapiens assay_type: microarray processed_data_available: true raw_data_availa... keyword match keyword match: homo sapiens

sample_type normal tissue GSM3933490 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal Normal 1 colonic mucosal sample tissue: colonic mucosa; diagnosis: healthy control controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM3933491 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal Normal 2 colonic mucosal sample tissue: colonic mucosa; diagnosis: healthy control controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM3933492 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal Normal 3 colonic mucosal sample tissue: colonic mucosa; diagnosis: healthy control controlled vocabulary controlled vocabulary sample type match: normal

tissue colon GSE134025 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence colonic dataset_accession: GSE134025 dataset_title: Ulcerative colitis gene expressions file organism: Homo sapiens assay_type: microarray processed_data_available: true raw_data_availa... controlled vocabulary controlled vocabulary tissue match: colonic

tissue colon GSM3933487 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence colonic UC patient 1 colonic mucosal sample tissue: colonic mucosa; diagnosis: ulcerative colitis controlled vocabulary controlled vocabulary tissue match: colonic

tissue colon GSM3933488 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence colonic UC patient 2 colonic mucosal sample tissue: colonic mucosa; diagnosis: ulcerative colitis controlled vocabulary controlled vocabulary tissue match: colonic

tissue colon GSM3933489 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence colonic UC patient 3 colonic mucosal sample tissue: colonic mucosa; diagnosis: ulcerative colitis controlled vocabulary controlled vocabulary tissue match: colonic

tissue colon GSM3933490 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence colonic Normal 1 colonic mucosal sample tissue: colonic mucosa; diagnosis: healthy control controlled vocabulary controlled vocabulary tissue match: colonic

tissue colon GSM3933491 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence colonic Normal 2 colonic mucosal sample tissue: colonic mucosa; diagnosis: healthy control controlled vocabulary controlled vocabulary tissue match: colonic

tissue colon GSM3933492 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence colonic Normal 3 colonic mucosal sample tissue: colonic mucosa; diagnosis: healthy control controlled vocabulary controlled vocabulary tissue match: colonic

Sample Group Preview

6 rows shown Show Hide

Study totals: Case 3 | Control 3 | Unassigned 0 | Excluded 0 | Ambiguous 0 6 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Ulcerative colitis	Case	GSM3933487	UC patient 1	Colonic mucosal sample Tissue: Colonic mucosa; Diagnosis: Ulcerative colitis	Case marker detected.
Ulcerative colitis	Case	GSM3933488	UC patient 2	Colonic mucosal sample Tissue: Colonic mucosa; Diagnosis: Ulcerative colitis	Case marker detected.
Ulcerative colitis	Case	GSM3933489	UC patient 3	Colonic mucosal sample Tissue: Colonic mucosa; Diagnosis: Ulcerative colitis	Case marker detected.
Healthy control	Control	GSM3933490	Normal 1	Colonic mucosal sample Tissue: Colonic mucosa; Diagnosis: Healthy control	Sample-local control marker detected.
Healthy control	Control	GSM3933491	Normal 2	Colonic mucosal sample Tissue: Colonic mucosa; Diagnosis: Healthy control	Sample-local control marker detected.
Healthy control	Control	GSM3933492	Normal 3	Colonic mucosal sample Tissue: Colonic mucosa; Diagnosis: Healthy 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

Intent Interpretation

Ranking Facts

Supporting evidence

Cautions

Dataset Warnings

Normalized Fields

Sample Group Preview

Use as Discovery Cohort