GSE65114

Expression data from colonic mucosal biopsies from healthy controls and patients with active ulcerative colitis

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

16 case / 12 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
28 samples
Specimen
Tissue
Reported/interpreted study design
Disease/model vs control Design classification does not establish patient pairs.
Comparison type
Tumor vs normal
Contributors
Balfe A, Lennon G, O'Connell R, Balfe AC
Contact name
Aine C Balfe
Submission date
2015-01-20
Last update
2019-03-15
Organization
University College Dublin
Department
School of Medicine and Medical Science
Public date
2015-01-21
Experiment types
Expression profiling by array
Platforms
GPL16686 [HuGene-2_0-st] Affymetrix Human Gene 2.0 ST Array [transcript (gene) version]
Series type
Series
SubSeries
Not available
BioProject
PRJNA273017

Summary

Expression data was used to evaluate changes to the transcriptional signatures across the healthy and inflamed colon. A comparison between healthy controls and active ulcerative colitis signatures was also made.

Overall design

Mucosal biopsy specimens were harvested at four anatomical locations within the colon from healthy volunteers and patients with active ulcerative colitis. specimens were fixed in RNA later for 24 hours at room temperature and stored at -80°C for a further 24 hours prior to RNA extraction and microarray analysis.

Source Evidence

4 sources
Source Contribution Status
GEO

Original dataset metadata, sample metadata, source links, and GEO data availability flags.

Sample records
28 GSM samples
 Primary source
recount3

Planned trusted source for processed count availability.

 No match found
Expression Atlas

Curated expression experiment linkage and source URL.

Expression Atlas accession
E-GEOD-65114
 Available
PubMed

Primary GEO citations and related PubMed articles that mention this dataset.

3 linked publications 3 DOIs

Related publications

  1. Identification of hub genes and immune infiltration in ulcerative colitis using bioinformatics. Scientific reports, 2023
  2. Screening of characteristic genes in ulcerative colitis by integrating gene expression profiles. BMC gastroenterology, 2021
  3. Development and Experimental Validation of Machine Learning-Based Disulfidptosis-Related Ferroptosis Biomarkers in Inflammatory Bowel Disease. Genes, 2025
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 16 samples
  • Likely control group Healthy control 12 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: Expression Atlas curated experiment link is available.
  • External evidence: PubMed links 3 publications; 3 DOIs available: PMID 34717557, PMID 37055495, PMID 40428318.
  • Publication context: Screening of characteristic genes in ulcerative colitis by integrating gene expression profiles.. BMC gastroenterology, 2021. PMID 34717557. DOI 10.1186/s12876-021-01940-0.
  • Publication context: Identification of hub genes and immune infiltration in ulcerative colitis using bioinformatics.. Scientific reports, 2023. PMID 37055495. DOI 10.1038/s41598-023-33292-y.
  • Publication context: Development and Experimental Validation of Machine Learning-Based Disulfidptosis-Related Ferroptosis Biomarkers in Inflammatory Bowel Disease.. Genes, 2025. PMID 40428318. DOI 10.3390/genes16050496.

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

Normalized Fields

76 fields

Sample Group Preview

28 rows shown Show Hide
Study totals: Case 16 | Control 12 | Unassigned 0 | Excluded 0 | Ambiguous 0 28 rows shown
Group Role Accession Title Source / characteristics Reason
Ulcerative colitis Case GSM1587529 Human Colonic Mucin from the caecum of patient with active ulcerative colitis AC_20_CAEC Human Colonic Mucin from patient with active ulcerative colitis Tissue source: Colon; Disease state: Active ulcerative colitis; Colonic location: Caecum Case marker detected.
Ulcerative colitis Case GSM1587530 Human Colonic Mucin from patient with active ulcerative colitis AC_20_LEFT Human Colonic Mucin from patient with active ulcerative colitis Tissue source: Colon; Disease state: Active ulcerative colitis; Colonic location: Left Case marker detected.
Ulcerative colitis Case GSM1587531 Human Colonic Mucin from patient with active ulcerative colitis AC_20_RECT Human Colonic Mucin from patient with active ulcerative colitis Tissue source: Colon; Disease state: Active ulcerative colitis; Colonic location: Rectum Case marker detected.
Ulcerative colitis Case GSM1587532 Human Colonic Mucin from the transverse colon of patient with active ulcerative colitis AC_20_TRANS Human Colonic Mucin from patient with active ulcerative colitis Tissue source: Colon; Disease state: Active ulcerative colitis; Colonic location: Transverse Case marker detected.
Ulcerative colitis Case GSM1587533 Human Colonic Mucin from the caecum of patient with active ulcerative colitis AC_21_CAEC Human Colonic Mucin from patient with active ulcerative colitis Tissue source: Colon; Disease state: Active ulcerative colitis; Colonic location: Caecum Case marker detected.
Ulcerative colitis Case GSM1587534 Human Colonic Mucin from patient with active ulcerative colitis AC_21_LEFT Human Colonic Mucin from patient with active ulcerative colitis Tissue source: Colon; Disease state: Active ulcerative colitis; Colonic location: Left Case marker detected.
Ulcerative colitis Case GSM1587535 Human Colonic Mucin from patient with active ulcerative colitis AC_21_RECT Human Colonic Mucin from patient with active ulcerative colitis Tissue source: Colon; Disease state: Active ulcerative colitis; Colonic location: Rectum Case marker detected.
Ulcerative colitis Case GSM1587536 Human Colonic Mucin from the transverse colon of patient with active ulcerative colitis AC_21_TRANS Human Colonic Mucin from patient with active ulcerative colitis Tissue source: Colon; Disease state: Active ulcerative colitis; Colonic location: Transverse Case marker detected.
Ulcerative colitis Case GSM1587537 Human Colonic Mucin from the caecum of patient with active ulcerative colitis AC_26_CAEC Human Colonic Mucin from patient with active ulcerative colitis Tissue source: Colon; Disease state: Active ulcerative colitis; Colonic location: Caecum Case marker detected.
Ulcerative colitis Case GSM1587538 Human Colonic Mucin from patient with active ulcerative colitis AC_26_LEFT Human Colonic Mucin from patient with active ulcerative colitis Tissue source: Colon; Disease state: Active ulcerative colitis; Colonic location: Left Case marker detected.
Ulcerative colitis Case GSM1587539 Human Colonic Mucin from patient with active ulcerative colitis AC_26_RECT Human Colonic Mucin from patient with active ulcerative colitis Tissue source: Colon; Disease state: Active ulcerative colitis; Colonic location: Rectum Case marker detected.
Ulcerative colitis Case GSM1587540 Human Colonic Mucin from the transverse colon of patient with active ulcerative colitis AC_26_TRANS Human Colonic Mucin from patient with active ulcerative colitis Tissue source: Colon; Disease state: Active ulcerative colitis; Colonic location: Transverse Case marker detected.
Ulcerative colitis Case GSM1587541 Human Colonic Mucin from the caecum of patient with active ulcerative colitis AC_28_CAEC Human Colonic Mucin from patient with active ulcerative colitis Tissue source: Colon; Disease state: Active ulcerative colitis; Colonic location: Caecum Case marker detected.
Ulcerative colitis Case GSM1587542 Human Colonic Mucin from patient with active ulcerative colitis AC_28_LEFT Human Colonic Mucin from patient with active ulcerative colitis Tissue source: Colon; Disease state: Active ulcerative colitis; Colonic location: Left Case marker detected.
Ulcerative colitis Case GSM1587543 Human Colonic Mucin from patient with active ulcerative colitis AC_28_RECT Human Colonic Mucin from patient with active ulcerative colitis Tissue source: Colon; Disease state: Active ulcerative colitis; Colonic location: Rectum Case marker detected.
Ulcerative colitis Case GSM1587544 Human Colonic Mucin from the transverse colon of patient with active ulcerative colitis AC_28_TRANS Human Colonic Mucin from patient with active ulcerative colitis Tissue source: Colon; Disease state: Active ulcerative colitis; Colonic location: Transverse Case marker detected.
Healthy control Control GSM1587517 Human Colonic Mucus from the caecum of Healthy controls HC_33_CAEC Human Colonic Mucin from Healthy controls Tissue source: Colon; Disease state: Healthy controls; Colonic location: Caecum Sample-local control marker detected.
Healthy control Control GSM1587518 Human Colonic Mucin from the left colon of Healthy controls HC_33_LEFT Human Colonic Mucin from Healthy controls Tissue source: Colon; Disease state: Healthy controls; Colonic location: Left Sample-local control marker detected.
Healthy control Control GSM1587519 Human Colonic Mucin from the rectum of Healthy controls HC_33_RECT Human Colonic Mucin from Healthy controls Tissue source: Colon; Disease state: Healthy controls; Colonic location: Rectum Sample-local control marker detected.
Healthy control Control GSM1587520 Human Colonic Mucin from the transverse colon of Healthy controls HC_33_TRANS Human Colonic Mucin from Healthy controls Tissue source: Colon; Disease state: Healthy controls; Colonic location: Transverse Sample-local control marker detected.
Healthy control Control GSM1587521 Human Colonic Mucin from the caecum of Healthy controls HC30_CAEC Human Colonic Mucin from Healthy controls Tissue source: Colon; Disease state: Healthy controls; Colonic location: Caecum Sample-local control marker detected.
Healthy control Control GSM1587522 Human Colonic Mucin from Healthy controls HC30_LEFT Human Colonic Mucin from Healthy controls Tissue source: Colon; Disease state: Healthy controls; Colonic location: Left Sample-local control marker detected.
Healthy control Control GSM1587523 Human Colonic Mucin from Healthy controls HC30_RECT Human Colonic Mucin from Healthy controls Tissue source: Colon; Disease state: Healthy controls; Colonic location: Rectum Sample-local control marker detected.
Healthy control Control GSM1587524 Human Colonic Mucin from the transverse colon of Healthy controls HC30_TRANS Human Colonic Mucin from Healthy controls Tissue source: Colon; Disease state: Healthy controls; Colonic location: Transverse Sample-local control marker detected.
Healthy control Control GSM1587525 Human Colonic Mucin from the caecum of Healthy controls HC31_CAEC Human Colonic Mucin from Healthy controls Tissue source: Colon; Disease state: Healthy controls; Colonic location: Caecum Sample-local control marker detected.
Healthy control Control GSM1587526 Human Colonic Mucin from Healthy controls HC31_LEFT Human Colonic Mucin from Healthy controls Tissue source: Colon; Disease state: Healthy controls; Colonic location: Left Sample-local control marker detected.
Healthy control Control GSM1587527 Human Colonic Mucin from Healthy controls HC31_RECT Human Colonic Mucin from Healthy controls Tissue source: Colon; Disease state: Healthy controls; Colonic location: Rectum Sample-local control marker detected.
Healthy control Control GSM1587528 Human Colonic Mucin from the transverse colon of Healthy controls HC31_TRANS Human Colonic Mucin from Healthy controls Tissue source: Colon; Disease state: Healthy controls; Colonic location: Transverse Sample-local control marker detected.

Use as Discovery Cohort

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