GSE279302

eQTL in diseased colon tissue identifies novel target genes associated with IBD

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

191 case / 0 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.

Summary

Genome-wide association studies (GWAS) have identified over 300 loci associated with the inflammatory bowel diseases (IBD), but putative causal genes for most are unknown. We conducted the largest disease-focused expression quantitative trait loci (eQTL) analysis using colon tissue from 252 IBD patients to determine genetic effects on gene expression and potential contribution to IBD. Combined with two non-IBD colon eQTL studies, we identified 194 potential target genes for 108 GWAS loci. eQTL in IBD tissue were enriched for IBD GWAS loci colocalizations, provided novel evidence for IBD-associated genes such as ABO and TNFRSF14, and identified additional target genes compared to non-IBD tissue eQTL. IBD-associated eQTL unique to diseased tissue had distinct regulatory and functional characteristics with increased effect sizes. Together, these highlight the importance of eQTL studies in diseased tissue for understanding functional consequences of genetic variants, and elucidating molecular mechanisms and regulation of key genes involved in IBD.

Overall design

RNA-seq of colon tissue from IBD patients for eQTL mapping *************************************************************** Submitter states that missing raw data are being made available for controlled access in dbGaP. ***************************************************************

Source Evidence

4 sources
Source Contribution Status
GEO

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

Sample records
191 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

Primary publication

  1. eQTL in diseased colon tissue identifies potential target genes associated with IBD. Nature communications, 2026
  2. eQTL in diseased colon tissue identifies novel target genes associated with IBD. bioRxiv : the preprint server for biology, 2024
Available

Metadata Quality Components

Analysis Readiness

Not ready
55% DE readiness

Contrast completeness

10/25 pts

Only one side of the contrast is present; downstream DE needs both groups.

Minimum group size

0/20 pts

Minimum group size cannot be evaluated until a complete contrast exists.

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

0/10 pts

Critical warnings must be resolved before downstream analysis.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

  • No complete case/control contrast is available.
  • Critical dataset warnings must be resolved.

Next Steps

  • Resolve critical warnings before downstream analysis.

Analysis Preparation Checklist

4/6 ready

Group labels reviewed

Blocked

No complete case/control grouping exists yet.

Review the sample grouping table and assign both case and control groups.

Minimum sample count met

Blocked

At least one group has fewer than 2 samples.

Choose a larger dataset or merge only scientifically valid groups.

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.

Analysis preparation checklist contains blocked items.

No complete case/control or treatment/control contrast is available.

At least one comparison group has fewer than two samples.

Critical dataset warnings are present.

Study design is model-system or unclear and should be reviewed before 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

  • Disease context Inflammatory bowel disease Disease context came from Normalization rules.
  • Likely case group Inflammatory bowel disease 191 samples
  • Likely control group No control group detected 0 samples

Intent Interpretation

  • Downgrade or exclusion reason Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

  • Prioritized assay: bulk RNA-seq is the active assay expectation.
  • Interpreted disease metadata: Inflammatory bowel disease.
  • Processed data is available for downstream review.
  • External evidence: PubMed links 2 publications; 2 DOIs available: PMID 39464142, PMID 41688467.
  • Publication context: eQTL in diseased colon tissue identifies novel target genes associated with IBD.. bioRxiv : the preprint server for biology, 2024. PMID 39464142. DOI 10.1101/2024.10.14.618229.
  • Publication context: eQTL in diseased colon tissue identifies potential target genes associated with IBD.. Nature communications, 2026. PMID 41688467. DOI 10.1038/s41467-026-69364-6.

Cautions

  • Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%.
  • Downgraded for tissue search because study design or specimen source is unclear.
  • Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
  • Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Missing or unclear metadata. Comparison - Unclear study design. Specimen - Tissue. Comparison suitability: 0%.
  • Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

Normalized Fields

showing 500 of 577 fields

Sample Group Preview

showing 50 of 191 preview rows
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Study totals: Case 191 | Control 0 | Unassigned 0 | Excluded 0 | Ambiguous 0 showing 50 of 191 preview rows
Group Role Accession Title Source / characteristics Reason
Inflammatory bowel disease Case GSM8566050 IBD_325497, colon Colon Tissue: Colon; Disease: IBD; Gender: Female; Batch: N Case marker detected.
Inflammatory bowel disease Case GSM8566051 IBD_916688, colon Colon Tissue: Colon; Disease: IBD; Gender: Male; Batch: N Case marker detected.
Inflammatory bowel disease Case GSM8566052 IBD_248736, colon Colon Tissue: Colon; Disease: IBD; Gender: Male; Batch: N Case marker detected.
Inflammatory bowel disease Case GSM8566053 IBD_271984, colon Colon Tissue: Colon; Disease: IBD; Gender: Female; Batch: H Case marker detected.
Inflammatory bowel disease Case GSM8566054 IBD_727218, colon Colon Tissue: Colon; Disease: IBD; Gender: Female; Batch: N Case marker detected.
Inflammatory bowel disease Case GSM8566055 IBD_296868, colon Colon Tissue: Colon; Disease: IBD; Gender: Female; Batch: I Case marker detected.
Inflammatory bowel disease Case GSM8566056 IBD_974304, colon Colon Tissue: Colon; Disease: IBD; Gender: Female; Batch: I Case marker detected.
Inflammatory bowel disease Case GSM8566057 IBD_900592, colon Colon Tissue: Colon; Disease: IBD; Gender: Male; Batch: I Case marker detected.
Inflammatory bowel disease Case GSM8566058 IBD_571968, colon Colon Tissue: Colon; Disease: IBD; Gender: Female; Batch: I Case marker detected.
Inflammatory bowel disease Case GSM8566059 IBD_124014, colon Colon Tissue: Colon; Disease: IBD; Gender: Female; Batch: I Case marker detected.
Inflammatory bowel disease Case GSM8566060 IBD_230729, colon Colon Tissue: Colon; Disease: IBD; Gender: Female; Batch: R Case marker detected.
Inflammatory bowel disease Case GSM8566061 IBD_779104, colon Colon Tissue: Colon; Disease: IBD; Gender: Female; Batch: N Case marker detected.
Inflammatory bowel disease Case GSM8566062 IBD_303678, colon Colon Tissue: Colon; Disease: IBD; Gender: Male; Batch: R Case marker detected.
Inflammatory bowel disease Case GSM8566063 IBD_123257, colon Colon Tissue: Colon; Disease: IBD; Gender: Female; Batch: R Case marker detected.
Inflammatory bowel disease Case GSM8566064 IBD_607036, colon Colon Tissue: Colon; Disease: IBD; Gender: Female; Batch: N Case marker detected.
Inflammatory bowel disease Case GSM8566065 IBD_150644, colon Colon Tissue: Colon; Disease: IBD; Gender: Female; Batch: HS4000_V1 Case marker detected.
Inflammatory bowel disease Case GSM8566066 IBD_664409, colon Colon Tissue: Colon; Disease: IBD; Gender: Male; Batch: HS4000_V1 Case marker detected.
Inflammatory bowel disease Case GSM8566067 IBD_268860, colon Colon Tissue: Colon; Disease: IBD; Gender: Male; Batch: HS4000_V1 Case marker detected.
Inflammatory bowel disease Case GSM8566068 IBD_105888, colon Colon Tissue: Colon; Disease: IBD; Gender: Female; Batch: HS4000_V1 Case marker detected.
Inflammatory bowel disease Case GSM8566069 IBD_383068, colon Colon Tissue: Colon; Disease: IBD; Gender: Male; Batch: HS4000_V1 Case marker detected.
Inflammatory bowel disease Case GSM8566070 IBD_336603, colon Colon Tissue: Colon; Disease: IBD; Gender: Male; Batch: I Case marker detected.
Inflammatory bowel disease Case GSM8566071 IBD_328631, colon Colon Tissue: Colon; Disease: IBD; Gender: Male; Batch: H Case marker detected.
Inflammatory bowel disease Case GSM8566072 IBD_602009, colon Colon Tissue: Colon; Disease: IBD; Gender: Female; Batch: I Case marker detected.
Inflammatory bowel disease Case GSM8566073 IBD_816534, colon Colon Tissue: Colon; Disease: IBD; Gender: Female; Batch: H Case marker detected.
Inflammatory bowel disease Case GSM8566074 IBD_771279, colon Colon Tissue: Colon; Disease: IBD; Gender: Male; Batch: H Case marker detected.
Inflammatory bowel disease Case GSM8566075 IBD_467982, colon Colon Tissue: Colon; Disease: IBD; Gender: Male; Batch: H Case marker detected.
Inflammatory bowel disease Case GSM8566076 IBD_396332, colon Colon Tissue: Colon; Disease: IBD; Gender: Male; Batch: I Case marker detected.
Inflammatory bowel disease Case GSM8566077 IBD_794755, colon Colon Tissue: Colon; Disease: IBD; Gender: Male; Batch: H Case marker detected.
Inflammatory bowel disease Case GSM8566078 IBD_919154, colon Colon Tissue: Colon; Disease: IBD; Gender: Female; Batch: H Case marker detected.
Inflammatory bowel disease Case GSM8566079 IBD_555519, colon Colon Tissue: Colon; Disease: IBD; Gender: Male; Batch: H Case marker detected.
Inflammatory bowel disease Case GSM8566080 IBD_484581, colon Colon Tissue: Colon; Disease: IBD; Gender: Male; Batch: H Case marker detected.
Inflammatory bowel disease Case GSM8566081 IBD_839147, colon Colon Tissue: Colon; Disease: IBD; Gender: Female; Batch: H Case marker detected.
Inflammatory bowel disease Case GSM8566082 IBD_595632, colon Colon Tissue: Colon; Disease: IBD; Gender: Female; Batch: R Case marker detected.
Inflammatory bowel disease Case GSM8566083 IBD_135118, colon Colon Tissue: Colon; Disease: IBD; Gender: Male; Batch: H Case marker detected.
Inflammatory bowel disease Case GSM8566084 IBD_954059, colon Colon Tissue: Colon; Disease: IBD; Gender: Male; Batch: I Case marker detected.
Inflammatory bowel disease Case GSM8566085 IBD_193721, colon Colon Tissue: Colon; Disease: IBD; Gender: Female; Batch: I Case marker detected.
Inflammatory bowel disease Case GSM8566086 IBD_560473, colon Colon Tissue: Colon; Disease: IBD; Gender: Male; Batch: I Case marker detected.
Inflammatory bowel disease Case GSM8566087 IBD_118727, colon Colon Tissue: Colon; Disease: IBD; Gender: Female; Batch: I Case marker detected.
Inflammatory bowel disease Case GSM8566088 IBD_301690, colon Colon Tissue: Colon; Disease: IBD; Gender: Female; Batch: I Case marker detected.
Inflammatory bowel disease Case GSM8566089 IBD_850257, colon Colon Tissue: Colon; Disease: IBD; Gender: Female; Batch: I Case marker detected.
Inflammatory bowel disease Case GSM8566090 IBD_268458, colon Colon Tissue: Colon; Disease: IBD; Gender: Female; Batch: I Case marker detected.
Inflammatory bowel disease Case GSM8566091 IBD_631005, colon Colon Tissue: Colon; Disease: IBD; Gender: Female; Batch: I Case marker detected.
Inflammatory bowel disease Case GSM8566092 IBD_346821, colon Colon Tissue: Colon; Disease: IBD; Gender: Male; Batch: I Case marker detected.
Inflammatory bowel disease Case GSM8566093 IBD_187482, colon Colon Tissue: Colon; Disease: IBD; Gender: Male; Batch: I Case marker detected.
Inflammatory bowel disease Case GSM8566094 IBD_845356, colon Colon Tissue: Colon; Disease: IBD; Gender: Female; Batch: I Case marker detected.
Inflammatory bowel disease Case GSM8566095 IBD_564849, colon Colon Tissue: Colon; Disease: IBD; Gender: Female; Batch: I Case marker detected.
Inflammatory bowel disease Case GSM8566096 IBD_420609, colon Colon Tissue: Colon; Disease: IBD; Gender: Female; Batch: I Case marker detected.
Inflammatory bowel disease Case GSM8566097 IBD_955826, colon Colon Tissue: Colon; Disease: IBD; Gender: Male; Batch: I Case marker detected.
Inflammatory bowel disease Case GSM8566098 IBD_949169, colon Colon Tissue: Colon; Disease: IBD; Gender: Male; Batch: I Case marker detected.
Inflammatory bowel disease Case GSM8566099 IBD_112415, colon Colon Tissue: Colon; Disease: IBD; Gender: Male; Batch: I Case marker detected.
141 additional case samples are hidden from this preview.

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.