GSE42911

Expression data in colon mucosa samples from individuals with ulcerative colitis and normal controls

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

5 case / 5 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: 10 samples
Specimen: Tissue
Reported/interpreted study design: Disease/model vs control Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Kellermayer R, Harris RA
Contact name: R. Alan Harris
Submission date: 2012-12-13
Last update: 2022-03-28
Organization: Baylor College of Medicine
Department: Molecular and Human Genetics
Public date: 2015-01-01
Experiment types: Expression profiling by array
Platforms: GPL15207 [PrimeView] Affymetrix Human Gene Expression Array
Series type: Series
SubSeries: Not available
BioProject: PRJNA183856

Summary

Genome wide expression profiling of ulcerative colitis, and normal colon mucosa samples. The GeneChip PrimeView Human Gene Expression Array was used to obtain expresion profiles across colon mucosa samples. Samples came from 5 ulcerative colitis affected, and 5 normal individuals.

Overall design

RNA from the 10 samples were hybridized to the GeneChip PrimeView Human Gene Expression Array

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 10 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 DNA methylation-associated colonic mucosal immune and defense responses in treatment-naïve pediatric ulcerative colitis. Epigenetics, 2014 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

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 5 samples
Likely control group Healthy control 5 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 1 publication; 1 DOI available: PMID 24937444.
Publication context: DNA methylation-associated colonic mucosal immune and defense responses in treatment-naïve pediatric ulcerative colitis.. Epigenetics, 2014. PMID 24937444. DOI 10.4161/epi.29446.

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 microarray cohorts should be compared separately from RNA-seq cohorts.
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

44 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source colon GSM1053268 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: colon mucosa 296 sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM1053268 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon mucosa source_name: colon mucosa 296 sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1053269 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: colon mucosa 206 sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM1053269 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon mucosa source_name: colon mucosa 206 sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1053270 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: colon mucosa 330 sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM1053270 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon mucosa source_name: colon mucosa 330 sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1053271 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: colon mucosa 395 sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM1053271 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon mucosa source_name: colon mucosa 395 sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1053272 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: colon mucosa 416 sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM1053272 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon mucosa source_name: colon mucosa 416 sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1053273 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: colon mucosa 397 sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM1053273 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon mucosa source_name: colon mucosa 397 sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1053274 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: colon mucosa 419 sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM1053274 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon mucosa source_name: colon mucosa 419 sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1053275 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: colon mucosa 429 sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM1053275 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon mucosa source_name: colon mucosa 429 sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1053276 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: colon mucosa 434 sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM1053276 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon mucosa source_name: colon mucosa 434 sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1053277 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: colon mucosa 432 sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM1053277 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon mucosa source_name: colon mucosa 432 sample-anatomical-source-v1 sample-local anatomical source

assay_type microarray GSE42911 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence microarray dataset_accession: GSE42911 dataset_title: Expression data in colon mucosa samples from individuals with ulcerative colitis and normal controls organism: Homo sapiens assay_type... keyword match keyword match: microarray

disease ulcerative colitis GSE42911 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis dataset_accession: GSE42911 dataset_title: Expression data in colon mucosa samples from individuals with ulcerative colitis and normal controls organism: Homo sapiens assay_type... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1053271 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Expression in colon mucosa 395 colon mucosa 395 gender: Female; age: 12; sample type: Colon mucosa; disease state: Ulcerative colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1053272 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Expression in colon mucosa 416 colon mucosa 416 gender: Male; age: 16; sample type: Colon mucosa; disease state: Ulcerative colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1053273 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Expression in colon mucosa 397 colon mucosa 397 gender: Male; age: 11; sample type: Colon mucosa; disease state: Ulcerative colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1053274 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Expression in colon mucosa 419 colon mucosa 419 gender: Female; age: 13; sample type: Colon mucosa; disease state: Ulcerative colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1053277 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Expression in colon mucosa 432 colon mucosa 432 gender: Female; age: 5; sample type: Colon mucosa; disease state: Ulcerative colitis controlled vocabulary controlled vocabulary disease match: ulcerative colitis

organism Homo sapiens GSE42911 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE42911 dataset_title: Expression data in colon mucosa samples from individuals with ulcerative colitis and normal controls organism: Homo sapiens assay_type... keyword match keyword match: homo sapiens

sample_type normal tissue GSM1053268 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal Expression in colon mucosa 296 colon mucosa 296 gender: Female; age: 9; sample type: Colon mucosa; disease state: normal controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM1053269 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal Expression in colon mucosa 206 colon mucosa 206 gender: Female; age: 15; sample type: Colon mucosa; disease state: normal controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM1053270 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal Expression in colon mucosa 330 colon mucosa 330 gender: Female; age: 16; sample type: Colon mucosa; disease state: normal controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM1053275 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal Expression in colon mucosa 429 colon mucosa 429 gender: Male; age: 17; sample type: Colon mucosa; disease state: normal controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM1053276 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal Expression in colon mucosa 434 colon mucosa 434 gender: Male; age: 17; sample type: Colon mucosa; disease state: normal controlled vocabulary controlled vocabulary sample type match: normal

tissue colon GSE42911 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon dataset_accession: GSE42911 dataset_title: Expression data in colon mucosa samples from individuals with ulcerative colitis and normal controls organism: Homo sapiens assay_type... controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1053268 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Expression in colon mucosa 296 colon mucosa 296 gender: Female; age: 9; sample type: Colon mucosa; disease state: normal controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1053269 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Expression in colon mucosa 206 colon mucosa 206 gender: Female; age: 15; sample type: Colon mucosa; disease state: normal controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1053270 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Expression in colon mucosa 330 colon mucosa 330 gender: Female; age: 16; sample type: Colon mucosa; disease state: normal controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1053271 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Expression in colon mucosa 395 colon mucosa 395 gender: Female; age: 12; sample type: Colon mucosa; disease state: Ulcerative colitis controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1053272 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Expression in colon mucosa 416 colon mucosa 416 gender: Male; age: 16; sample type: Colon mucosa; disease state: Ulcerative colitis controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1053273 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Expression in colon mucosa 397 colon mucosa 397 gender: Male; age: 11; sample type: Colon mucosa; disease state: Ulcerative colitis controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1053274 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Expression in colon mucosa 419 colon mucosa 419 gender: Female; age: 13; sample type: Colon mucosa; disease state: Ulcerative colitis controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1053275 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Expression in colon mucosa 429 colon mucosa 429 gender: Male; age: 17; sample type: Colon mucosa; disease state: normal controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1053276 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Expression in colon mucosa 434 colon mucosa 434 gender: Male; age: 17; sample type: Colon mucosa; disease state: normal controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1053277 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Expression in colon mucosa 432 colon mucosa 432 gender: Female; age: 5; sample type: Colon mucosa; disease state: Ulcerative colitis controlled vocabulary controlled vocabulary tissue match: colon

Sample Group Preview

10 rows shown Show Hide

Study totals: Case 5 | Control 5 | Unassigned 0 | Excluded 0 | Ambiguous 0 10 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Ulcerative colitis	Case	GSM1053271	Expression in colon mucosa 395	Colon mucosa 395 Gender: Female; Age: 12; Sample type: Colon mucosa; Disease state: Ulcerative colitis	Case marker detected.
Ulcerative colitis	Case	GSM1053272	Expression in colon mucosa 416	Colon mucosa 416 Gender: Male; Age: 16; Sample type: Colon mucosa; Disease state: Ulcerative colitis	Case marker detected.
Ulcerative colitis	Case	GSM1053273	Expression in colon mucosa 397	Colon mucosa 397 Gender: Male; Age: 11; Sample type: Colon mucosa; Disease state: Ulcerative colitis	Case marker detected.
Ulcerative colitis	Case	GSM1053274	Expression in colon mucosa 419	Colon mucosa 419 Gender: Female; Age: 13; Sample type: Colon mucosa; Disease state: Ulcerative colitis	Case marker detected.
Ulcerative colitis	Case	GSM1053277	Expression in colon mucosa 432	Colon mucosa 432 Gender: Female; Age: 5; Sample type: Colon mucosa; Disease state: Ulcerative colitis	Case marker detected.
Healthy control	Control	GSM1053268	Expression in colon mucosa 296	Colon mucosa 296 Gender: Female; Age: 9; Sample type: Colon mucosa; Disease state: Normal	Sample-local control marker detected.
Healthy control	Control	GSM1053269	Expression in colon mucosa 206	Colon mucosa 206 Gender: Female; Age: 15; Sample type: Colon mucosa; Disease state: Normal	Sample-local control marker detected.
Healthy control	Control	GSM1053270	Expression in colon mucosa 330	Colon mucosa 330 Gender: Female; Age: 16; Sample type: Colon mucosa; Disease state: Normal	Sample-local control marker detected.
Healthy control	Control	GSM1053275	Expression in colon mucosa 429	Colon mucosa 429 Gender: Male; Age: 17; Sample type: Colon mucosa; Disease state: Normal	Sample-local control marker detected.
Healthy control	Control	GSM1053276	Expression in colon mucosa 434	Colon mucosa 434 Gender: Male; Age: 17; Sample type: Colon mucosa; Disease state: Normal	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

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