Ranked GEO Datasets

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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.

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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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11 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 10 of 10 · showing 136-146

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.

Gene expression signature and mitochondrial DNA copy number variation in ulcerative colitis patients

Select

Organization: University of Tokyo

Case ulcerative colitis Control unclear

Unclear study design Tissue

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded for tissue search because study design or specimen source is unclear.
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 28652445, PMID 35705632.

critical No clear control group was detected from normalized metadata. 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. warning Patient-tissue tumor-normal intent requires clear tumor-normal grouping.

A long noncoding RNA signature in Ulcerative Colitis

Select

Organization: UCLA

Case ulcerative colitis Control unclear

Unclear study design Tissue

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded for tissue search because study design or specimen source is unclear.
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 27492330.

critical No clear control group was detected from normalized metadata. 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. warning Patient-tissue tumor-normal intent requires clear tumor-normal grouping.

Gene expression profiling of mucosal biopsies from pediatric patients with moderately to severely active ulcerative colitis

Select

Organization: Janssen R&D

Case ulcerative colitis Control unclear

Unclear study design Biopsy

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded for tissue search because study design or specimen source is unclear.
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 29401083.

critical No clear control group was detected from normalized metadata. 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. warning Patient-tissue tumor-normal intent requires clear tumor-normal grouping.

Inflammatory Bowel Disease-specific alterations in adipose-derived stroma cell transcriptional profiles

Select

Organization: UCLA, David Geffen School of Medicine

Case mixed disease cohort Control 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.

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.

IPA analysis of CD14-positive monocytes/macrophages from IBD patients and controls

Select

Organization: Friedrich-Alexander University Erlangen-Nuremberg

Case inflammatory bowel disease Control control

Disease/model vs control Unclear specimen/source

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded for tissue search because study design or specimen source is unclear.
Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Interpreted disease metadata: Inflammatory bowel disease.
Processed data is available for downstream review.

info Microarray expression context was detected; compare separately from RNA-seq cohorts. warning Tissue or cell type could not be normalized. warning Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. warning Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.

Exon Array Analysis of Asthmatic Chronic Rhinosinusitis with Nasal Polyps

Select

Organization: Mayo Clinic Rochester

Case mixed disease cohort 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: Asthma, Inflammatory bowel disease.
Processed data is available for downstream review.
External evidence: PubMed links 6 publications; 5 DOIs available: PMID 20625511, PMID 33603773, PMID 36059464, PMID 36915741, PMID 39986126.

Impact of NOD2 Genotype on the Innate Monocyte Transcriptome in Crohn’s Disease

Select

Organization: Chr Hansen A/S

Case treated Control untreated

Treatment vs control Unclear specimen/source

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 for tissue search because study design or specimen source is unclear.
Prioritized assay: bulk RNA-seq is the active assay expectation.
Interpreted disease metadata: Crohn's disease.
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 29263823.

info Treated samples may need review depending on the comparison. info Treated and untreated samples are both present. warning Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected. warning Tissue or cell type could not be normalized. warning Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.

Macrophages in Crohn’s disease creeping fat are predominantly inflammatory and produce calprotectin

Select

Organization: Amsterdam UMC

Case mixed disease cohort Control unclear

Unclear study design Unclear specimen/source

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded for tissue search because study design or specimen source is unclear.
Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Interpreted disease metadata: Crohn's disease, Ulcerative colitis.
Processed data is available for downstream review.

critical No clear control group was detected from normalized metadata. info Microarray expression context was detected; compare separately from RNA-seq cohorts. warning Tissue or cell type could not be normalized. 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. warning Patient-tissue tumor-normal intent requires clear tumor-normal grouping. warning Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.

Pro- and anti-tumorigenic capacity of immunoproteasomes in shaping the tumor microenvironment

Select

Organization: Max-Planck-Institute for Infection Biology

Case unclear Control mixed controls

Unclear study design Tissue

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded for tissue search because study design or specimen source is unclear.
Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Interpreted disease metadata: Melanoma, Ulcerative colitis.
Processed data is available for downstream review.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 33707310.

warning Dataset has fewer than six samples and should not be treated as a high-confidence cohort without manual review. 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. warning Patient-tissue tumor-normal intent requires clear tumor-normal grouping.

Mediators in Crohn’s disease influence the gene expression profiles of mesenchymal progenitor cells differentiated into the osteoblastic lineage.

Select

Organization: Universitaetsmedizin Goettingen

Case mixed disease cohort Control unclear

Unclear study design Tissue

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded for tissue search because study design or specimen source is unclear.
Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Interpreted disease metadata: Crohn's disease.
Processed data is available for downstream review.

critical No clear control group was detected from normalized metadata. 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. warning Patient-tissue tumor-normal intent requires clear tumor-normal grouping.

Genome-wide analysis of monocyte derived macrophages from Crohn's Disease patients and controls

Select

Organization: UCL

Case unclear Control untreated

Unclear study design Cultured cells

Rationale for Tumor vs normal

Dataset does not meet the current suitability threshold.

Downgraded for tissue search because it is a model-system experiment.
Downgraded for tissue search because study design or specimen source is unclear.
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 24943399.

info Microarray expression context was detected; compare separately from RNA-seq cohorts. warning Cultured primary, endothelial, macrophage, or stem-cell samples were detected; interpret these as an experimental model rather than a patient biofluid or tissue cohort. warning Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled. warning Patient-tissue tumor-normal intent requires clear tumor-normal grouping.