Ranked GEO Datasets

Collections related to this search

Explore premium collections with reusable study, cohort and sample curation. The matching scope is stated for each collection. Organism, tissue, comparison and sample requirements still need review; collection availability does not affect dataset ranking.

IBD Colon Tissue Expression Collection

Disease scope matches your disease term.

Public colon tissue expression datasets for IBD, Crohn's disease, and ulcerative colitis.

Preview fixture · Version v0.1-preview

Study inventory: 3 datasets
Reported sample inventory: 522 samples
Updated: 2026-06-22
Disease: Inflammatory bowel disease
Organisms: Homo sapiens
Technologies: microarray, bulk RNA-seq
Tissues: colon biopsy, inflamed colon tissue, non-inflamed colon tissue
Comparisons: IBD vs non-IBD control, inflamed vs non-inflamed tissue, Crohn's disease vs ulcerative colitis

Query overlap with this collection version
Dimension	Your query	Collection scope	Comparison
Disease	Inflammatory bowel disease	Inflammatory bowel disease	MATCH Declared collection scope includes this requested dimension; question-specific sample eligibility still needs review.
Specimen		colon biopsy, inflamed colon tissue, non-inflamed colon tissue	NOT_REQUESTED No explicit query requirement was supplied for this dimension.
Organism		Homo sapiens	NOT_REQUESTED No explicit query requirement was supplied for this dimension.
Comparison		IBD vs non-IBD control, inflamed vs non-inflamed tissue, Crohn's disease vs ulcerative colitis	NOT_REQUESTED No explicit query requirement was supplied for this dimension.

Full access adds reusable curated cohort structure, sample decisions and provenance. Review the content status above before treating a release as professionally approved. Ordinary Search results remain available below.

Preview collection

Counts describe the collection inventory, not final eligible samples or independent subjects. Preview fixtures are illustrative; review-pending releases are not professionally approved.

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15 shown of 146 matching datasets Comparison Tumor vs normal Tissue/sample context Patient tissue Organism Any organism Assay Any assay Ranking defaults Modified 6 user changes 1 active filters Page 1 of 10 · showing 1-15

Disease/condition e.g. colorectal cancer Anatomical source Specimen material Cell population Comparison type (required) Organism Assay type Minimum samples Experimental model Exclude cell lines Require processed data GEO only recount3 available Expression Atlas available

Treatment requirements Optional See what each comparison arm must satisfy — Unrestricted

Comparison: Tumor vs normal

Case arm

Your requirement

Exposure state

Agent

Comparator

From comparison

Determined by comparison

For treatment vs control, use a named agent, an explicit collection window and an exposed or unexposed state. The comparator needs the opposite reported exposure state for the same agent, target and window.

Collection window Assertion target

Named agent if supplied; otherwise all interventions.

Scope & matching · additional options

Exposure scopeAutomatic: named agent if supplied; otherwise all interventions. Uncertain alternativesReview cases are not confirmed matches. Exact reported scope (when requested)

Missing metadata never proves no exposure.

Evidence and comparison rules

Exact results require an eligible sample subset and reported independent subjects in both arms.

“No exposure” applies only to the selected agent, target and time window. No exposure to a new agent before collection does not rule out earlier therapy.

A broader treatment history requires separate, explicit evidence and may be unavailable. All prior therapy requires a through-collection window.

Planned exposure does not establish that treatment occurred. Treatment vs control requires an exposed or unexposed state, a named agent and an explicit collection window.

Organism and specimen requirements apply to both arms. For treatment vs control, disease requirements also apply to both arms.

Genotype requirements Optional Define a requirement, then assign it to samples — Unrestricted

Genetic state Gene symbol

Apply requirement to

Specific protein variant · optional

Exact reported protein variant

Leave blank for a gene-level requirement. A variant restriction applies to every selected arm.

Genotype describes sampled material. Confirmed evidence must come from the same samples as your other requirements.

Use with human bulk RNA-seq or expression microarray.

Evidence and comparison rules

Select Homo sapiens and a supported assay in the search filters.

Missing genotype does not establish wild type. Both comparison arms still need eligible, independent samples.

A subject's carrier status does not establish the sampled tumor's genotype or disease.

Clear filters Ranking defaults Relax defaults

Showing one page of matching results. Use next/previous for browsing, or CSV/Markdown export for the full matching set.

Strict results

These datasets meet every active search criterion.

Genome-wide analysis of colorectal cancer gene expression by using primary tumors, normal colon and lymph nodes

Select

Organization: Umeå universitet

Case mixed disease cohort Control control

Tumor vs normal; consult patient linkage Tissue

Rationale for Tumor vs normal

Scores are usable, but sample metadata contains review-only concerns.

Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Interpreted disease metadata: Colorectal cancer, Crohn's disease, Ulcerative colitis.
Processed data is available for downstream review.
External evidence: PubMed links 4 publications; 4 DOIs available: PMID 32049988, PMID 38747892, PMID 39661280, PMID 41747601.

info Microarray expression context was detected; compare separately from RNA-seq cohorts. warning Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis. warning Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.

Expression of long non-coding RNAs in autoimmunity and linkage to enhancer function and autoimmune disease risk genetic variants

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Organization: Vanderbilt University School of Medicine

Case ulcerative colitis Control healthy control

Patient biofluid vs healthy control Biofluid

Rationale for Tumor vs normal

Dataset can inform exploration but is not strong enough for primary analysis.

Downgraded for tissue search because it is a biofluid cohort.
Prioritized assay: bulk RNA-seq is the active assay expectation.
Interpreted disease metadata: Crohn's disease, Lupus erythematosus, Sjogren syndrome, Systemic lupus erythematosus, Ulcerative colitis.
Processed data is available for downstream review.
External evidence: recount3 reports trusted processed count availability.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 28420548.

No warnings

A functional genomics predictive network model identifies regulators of inflammatory bowel disease: Microarray Analysis of Human Blood and Intestinal Biopsy Samples from a Phase 2b, Double-blind, Placebo-controlled Study of Ustekinumab in Crohn's Disease

Select

Organization: Icahn School of Medicine at Mount Sinai

Case mixed disease cohort Control healthy control

Treatment vs control Mixed specimen/source

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded for tissue search because specimen/source classes are mixed.
Downgraded for tissue search because it is a treatment/control experiment.
Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Interpreted disease metadata: Crohn's disease, Inflammatory bowel disease.
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 32612148, PMID 36685554, PMID 39894009.

Mucosal gene expression profiling in ileum of patients with Crohn's disease

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Organization: KU Leuven

Case Crohn's disease Control healthy control

Disease/model vs control Biopsy

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Interpreted disease metadata: Crohn's disease.
Processed data is available for downstream review.
External evidence: Expression Atlas curated experiment link is available.
External evidence: PubMed links 9 publications; 9 DOIs available: PMID 30657881, PMID 36118873, PMID 36714107, PMID 36742294, PMID 38274342.

info Microarray expression context was detected; compare separately from RNA-seq cohorts. warning Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.

Human colon expression in healthy controls, colon-only CD, ileo-colonic CD, and UC

Select

Organization: CCHMC

Case Crohn's disease Control healthy control

Disease/model vs control Tissue

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Interpreted disease metadata: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis.
Processed data is available for downstream review.
External evidence: PubMed links 7 publications; 7 DOIs available: PMID 18758464, PMID 29401083, PMID 36479126, PMID 36860851, PMID 37275904.

Expression data from Ulcerative Colitis subjects

Select

Organization: Pfizer Inc

Case lesional tissue Control non-lesional tissue

Disease/model vs control Biopsy

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Interpreted disease metadata: Ulcerative colitis.
Processed data is available for downstream review.
External evidence: PubMed links 10 publications; 10 DOIs available: PMID 32566650, PMID 32871953, PMID 34997010, PMID 36742294, PMID 37842511.

Gene expression profiles in sigmoid colon biopsies from healthy and patients with ulcerative colitis

Select

Organization: Johns Hopkins Univ

Case ulcerative colitis Control healthy control

Disease/model vs control Biopsy

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Interpreted disease metadata: Ulcerative colitis.
Processed data is available for downstream review.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 18835392.

warning Total sample count is below the minimum needed for two comparison groups. info Microarray expression context was detected; compare separately from RNA-seq cohorts. warning Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.

NOD2- and disease-specific gene expression profiles of peripheral blood mononuclear cells from Crohn’s disease patients

Select

Organization: University of Rostock

Case treated Control healthy control

Treatment vs control Biofluid

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded for tissue search because it is a biofluid cohort.
Downgraded for tissue search because it is a treatment/control experiment.
Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Interpreted disease metadata: Crohn's disease.
Processed data is available for downstream review.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 29568200.

Longitudinal Multi’omics of the Human Microbiome in Inflammatory Bowel Disease

Select

Organization: Harvard T.H. Chan School of Public Health

Case mixed disease cohort Control non-inflamed tissue

Disease/model vs control Biopsy

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Prioritized assay: bulk RNA-seq is the active assay expectation.
Interpreted disease metadata: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis.
Processed data is available for downstream review.
External evidence: PubMed links 3 publications; 3 DOIs available: PMID 31142855, PMID 33769280, PMID 35795659.

warning Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.

Whole Blood Transcriptome Profiling in Juvenile Idiopathic Arthritis and Inflammatory Bowel Disease

Select

Organization: Georgia Institute of Technology

Case Crohn's disease Control control

Disease/model vs control Biofluid

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded for tissue search because it is a biofluid cohort.
Prioritized assay: bulk RNA-seq is the active assay expectation.
Interpreted disease metadata: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis.
Processed data is available for downstream review.
External evidence: recount3 reports trusted processed count availability.
External evidence: Expression Atlas curated experiment link is available.
External evidence: PubMed links 3 publications; 3 DOIs available: PMID 29950172, PMID 34336925, PMID 39894009.

No warnings

Colon biopsies from UC patients and healthy controls

Select

Organization: Genentech, Inc.

Case treated Control mixed controls

Treatment vs control Biofluid

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded for tissue search because it is a biofluid cohort.
Downgraded for tissue search because it is a treatment/control experiment.
Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Interpreted disease metadata: Asthma, Breast cancer, Colorectal cancer, Crohn's disease, Inflammatory bowel disease, Prostate cancer, Ulcerative colitis.
Processed data is available for downstream review.
External evidence: PubMed links 4 publications; 4 DOIs available: PMID 18523026, PMID 25822611, PMID 37529244, PMID 39596612.

warning Multiple sample type labels or exclusion flags were detected. info Treated samples may need review depending on the comparison. info Microarray expression context was detected; compare separately from RNA-seq cohorts. warning Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.

Intestinal epithelial microvilli are abnormal in Crohn's disease

Select

Organization: Janssen R&D

Case treated Control healthy control

Treatment vs control Biopsy

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded for tissue search because it is a treatment/control experiment.
Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Interpreted disease metadata: Crohn's disease, Inflammatory bowel disease.
Processed data is available for downstream review.
External evidence: PubMed links 10 publications; 10 DOIs available: PMID 29782846, PMID 34469062, PMID 36817485, PMID 38521905, PMID 38840917.

Inflammatory bowel disease (HG-U133A)

Select

Organization: Institute of Human Genetics

Case Crohn's disease Control control

Disease/model vs control Biopsy

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Interpreted disease metadata: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis.
Processed data is available for downstream review.

Inflammatory bowel disease (HG-U133B)

Select

Organization: Institute of Human Genetics

Case inflammatory bowel disease Control control

Disease/model vs control Biopsy

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Interpreted disease metadata: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis.
Processed data is available for downstream review.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 39331894.

A systems biology approach identifies ANP32E and other biomarkers of glucocorticoid refractoriness in ulcerative colitis [microarray]

Select

Organization: CIC bioGUNE

Case ulcerative colitis Control healthy control

Disease/model vs control Tissue

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Interpreted disease metadata: Ulcerative colitis.
Processed data is available for downstream review.
External evidence: PubMed links 2 publications; 2 DOIs available: PMID 30329026, PMID 35705632.

warning Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. info Microarray expression context was detected; compare separately from RNA-seq cohorts. warning Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.