GSE3365

Comparison of PBMCs in Inflammatory Bowel Disease

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

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

Comparison of PBMC transcriptional profiles in healthy subjects, patients with Crohn's Disease, and patients with Ulcerative Colitis Keywords: Disease state

Overall design

Source Evidence

4 sources
Source Contribution Status
GEO

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

Sample records
127 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.

11 linked publications 11 DOIs

Primary publication

  1. Molecular classification of Crohn's disease and ulcerative colitis patients using transcriptional profiles in peripheral blood mononuclear cells. The Journal of molecular diagnostics : JMD, 2006

Related publications

  1. An Ensemble Classifier for Ordinal Outcomes in High-Dimensional Genomics Data. Pharmaceutical statistics, 2026
  2. Blood transcriptomics identifies FEZ1 as a potential biomarker for inflammatory bowel disease. Computers in biology and medicine, 2025
  3. Integrative bioinformatics and deep learning to identify common genetic pathways in Crohn's disease and ischemic cardiomyopathy. Journal, genetic engineering & biotechnology, 2025
  4. Investigating Immune Microenvironment of Inflammatory Bowel Disease and the Mitochondrial Metabolism-Related Molecular Mechanisms: Combining a Multiomics Approach and Experimental Validation. Omics : a journal of integrative biology, 2026
  5. Exploring the molecular mechanism of comorbidity of autism spectrum disorder and inflammatory bowel disease by combining multiple data sets. Journal of translational medicine, 2023
  6. Concordance between gene expression in peripheral whole blood and colonic tissue in children with inflammatory bowel disease. PloS one, 2019
  7. Discovery and Validation of Ferroptosis-Associated Genes of Ulcerative Colitis. Journal of inflammation research, 2024
  8. Common diagnostic biomarkers and molecular mechanisms of Helicobacter pylori infection and inflammatory bowel disease. Frontiers in immunology, 2024
  9. Identification of oxidative stress-associated biomarkers for inflammatory bowel disease through integrated machine learning and weighted gene co-expression network analysis. Frontiers in immunology, 2026
  10. Regulation of ulcerative colitis progression by ferroptosis pathway genes: HSP90AA1, SNCA, TLR4, and PTGS2. American journal of translational research, 2025
Available

Metadata Quality Components

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 Crohn's disease, inflammatory bowel disease, ulcerative colitis Disease context came from Normalization rules.
  • Likely case group Ulcerative colitis 85 samples
  • Likely control group Normal tissue 42 samples

Intent Interpretation

  • Downgrade or exclusion reason Downgraded for tissue search because it is a biofluid cohort. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

  • Comparison: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%.
  • Interpreted disease metadata: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis.
  • Processed data is available for downstream review.
  • External evidence: PubMed links 11 publications; 11 DOIs available: PMID 16436634, PMID 31618209, PMID 37291580, PMID 39006497, PMID 39712025.
  • Publication context: Molecular classification of Crohn's disease and ulcerative colitis patients using transcriptional profiles in peripheral blood mononuclear cells.. The Journal of molecular diagnostics : JMD, 2006. PMID 16436634. DOI 10.2353/jmoldx.2006.050079.
  • Publication context: Concordance between gene expression in peripheral whole blood and colonic tissue in children with inflammatory bowel disease.. PloS one, 2019. PMID 31618209. DOI 10.1371/journal.pone.0222952.
  • Publication context: Exploring the molecular mechanism of comorbidity of autism spectrum disorder and inflammatory bowel disease by combining multiple data sets.. Journal of translational medicine, 2023. PMID 37291580. DOI 10.1186/s12967-023-04218-z.
  • Publication context: 8 additional linked PubMed publications are available.

Cautions

  • Downgraded for tissue search because it is a biofluid cohort.
  • Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
  • Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
  • Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

Normalized Fields

showing 500 of 514 fields

Sample Group Preview

showing 92 of 127 preview rows
Show Hide
Study totals: Case 85 | Control 42 | Unassigned 0 | Excluded 0 | Ambiguous 0 showing 92 of 127 preview rows
Group Role Accession Title Source / characteristics Reason
Ulcerative colitis Case GSM76030 Ulcerative Colitis (55 year old black female, SAK_1285134540) PBMCs from Ulcerative Colitis subject None Case marker detected.
Ulcerative colitis Case GSM76031 Ulcerative Colitis (47 year old caucasian male, SAK_1286408661) PBMCs from Ulcerative Colitis subject None Case marker detected.
Ulcerative colitis Case GSM76032 Ulcerative Colitis (55 year old caucasian female, SAK_1319013894) PBMCs from Ulcerative Colitis subject None Case marker detected.
Ulcerative colitis Case GSM76033 Ulcerative Colitis (60 year old caucasian male, SAK_1305668541) PBMCs from Ulcerative Colitis subject None Case marker detected.
Ulcerative colitis Case GSM76034 Ulcerative Colitis (49 year old caucasian female, SAK_1286431014) PBMCs from Ulcerative Colitis subject None Case marker detected.
Ulcerative colitis Case GSM76035 Ulcerative Colitis (37 year old caucasian female, SAK_1286609838) PBMCs from Ulcerative Colitis subject None Case marker detected.
Ulcerative colitis Case GSM76036 Ulcerative Colitis (41 year old black female, SAK_1304707354) PBMCs from Ulcerative Colitis subject None Case marker detected.
Ulcerative colitis Case GSM76037 Ulcerative Colitis (25 year old caucasian female, SAK_1286453367) PBMCs from Ulcerative Colitis subject None Case marker detected.
Ulcerative colitis Case GSM76038 Ulcerative Colitis (45 year old caucasian male, SAK_1286475720) PBMCs from Ulcerative Colitis subject None Case marker detected.
Ulcerative colitis Case GSM76039 Ulcerative Colitis (30 year old black female, SAK_1286498073) PBMCs from Ulcerative Colitis subject None Case marker detected.
Ulcerative colitis Case GSM76040 Ulcerative Colitis (65 year old caucasian male, SAK_1291908052) PBMCs from Ulcerative Colitis subject None Case marker detected.
Ulcerative colitis Case GSM76041 Ulcerative Colitis (40 year old caucasian female, SAK_1285156893) PBMCs from Ulcerative Colitis subject None Case marker detected.
Ulcerative colitis Case GSM76042 Ulcerative Colitis (27 year old caucasian female, SAK_1286520426) PBMCs from Ulcerative Colitis subject None Case marker detected.
Ulcerative colitis Case GSM76043 Ulcerative Colitis (57 year old caucasian female, SAK_1286542779) PBMCs from Ulcerative Colitis subject None Case marker detected.
Ulcerative colitis Case GSM76044 Ulcerative Colitis (59 year old caucasian female, SAK_1286565132) PBMCs from Ulcerative Colitis subject None Case marker detected.
Ulcerative colitis Case GSM76045 Ulcerative Colitis (27 year old caucasian female, SAK_1286587485) PBMCs from Ulcerative Colitis subject None Case marker detected.
Ulcerative colitis Case GSM76046 Ulcerative Colitis (33 year old hispanic female, SAK_1285179246) PBMCs from Ulcerative Colitis subject None Case marker detected.
Ulcerative colitis Case GSM76047 Ulcerative Colitis (62 year old caucasian female, SAK_1305735600) PBMCs from Ulcerative Colitis subject None Case marker detected.
Ulcerative colitis Case GSM76048 Ulcerative Colitis (41 year old caucasian female, SAK_1318969188) PBMCs from Ulcerative Colitis subject None Case marker detected.
Ulcerative colitis Case GSM76049 Ulcerative Colitis (41 year old caucasian female, SAK_1285223952) PBMCs from Ulcerative Colitis subject None Case marker detected.
Ulcerative colitis Case GSM76050 Ulcerative Colitis (53 year old caucasian male, SAK_1285246305) PBMCs from Ulcerative Colitis subject None Case marker detected.
Ulcerative colitis Case GSM76051 Ulcerative Colitis (42 year old caucasian male, SAK_1285268658) PBMCs from Ulcerative Colitis subject None Case marker detected.
Ulcerative colitis Case GSM76052 Ulcerative Colitis (57 year old caucasian male, SAK_1285291011) PBMCs from Ulcerative Colitis subject None Case marker detected.
Ulcerative colitis Case GSM76053 Ulcerative Colitis (29 year old caucasian female, SAK_1305780306) PBMCs from Ulcerative Colitis subject None Case marker detected.
Ulcerative colitis Case GSM76054 Ulcerative Colitis (73 year old caucasian male, SAK_1285313364) PBMCs from Ulcerative Colitis subject None Case marker detected.
Ulcerative colitis Case GSM76055 Ulcerative Colitis (63 year old caucasian female, SAK_1318991541) PBMCs from Ulcerative Colitis subject None Case marker detected.
Crohn's disease Case GSM76056 Crohn's Disease subject (22 year old black female, SAK_1259740044) PBMCs from Crohn's Disease subject None Case marker detected.
Crohn's disease Case GSM76057 Crohn's Disease subject (46 year old black female, SAK_1259829456) PBMCs from Crohn's Disease subject None Case marker detected.
Crohn's disease Case GSM76058 Crohn's Disease subject (39 year old caucasian male, SAK_1275567445) PBMCs from Crohn's Disease subject None Case marker detected.
Crohn's disease Case GSM76059 Crohn's Disease subject (20 year old black male, SAK_1259851809) PBMCs from Crohn's Disease subject None Case marker detected.
Crohn's disease Case GSM76060 Crohn's Disease subject (47 year old caucasian male, SAK_1263137700) PBMCs from Crohn's Disease subject None Case marker detected.
Crohn's disease Case GSM76061 Crohn's Disease subject (56 year old caucasian male, SAK_1260008280) PBMCs from Crohn's Disease subject None Case marker detected.
Crohn's disease Case GSM76062 Crohn's Disease subject (41 year old caucasian female, SAK_1277825109) PBMCs from Crohn's Disease subject None Case marker detected.
Crohn's disease Case GSM76063 Crohn's Disease subject (21 year old caucasian male, SAK_1260634232) PBMCs from Crohn's Disease subject None Case marker detected.
Crohn's disease Case GSM76064 Crohn's Disease subject (33 year old caucasian male, SAK_1288174788) PBMCs from Crohn's Disease subject None Case marker detected.
Crohn's disease Case GSM76065 Crohn's Disease subject (64 year old caucasian female, SAK_1260745997) PBMCs from Crohn's Disease subject None Case marker detected.
Crohn's disease Case GSM76066 Crohn's Disease subject (29 year old caucasian female, SAK_1280865117) PBMCs from Crohn's Disease subject None Case marker detected.
Crohn's disease Case GSM76067 Crohn's Disease subject (42 year old black female, SAK_1287526311) PBMCs from Crohn's Disease subject None Case marker detected.
Crohn's disease Case GSM76068 Crohn's Disease subject (43 year old black male, SAK_1287548671) PBMCs from Crohn's Disease subject None Case marker detected.
Crohn's disease Case GSM76069 Crohn's Disease subject (47 year old caucasian female, SAK_1280820411) PBMCs from Crohn's Disease subject None Case marker detected.
Crohn's disease Case GSM76070 Crohn's Disease subject (39 year old caucasian female, SAK_1261237763) PBMCs from Crohn's Disease subject None Case marker detected.
Crohn's disease Case GSM76071 Crohn's Disease subject (33 year old caucasian male, SAK_1280753352) PBMCs from Crohn's Disease subject None Case marker detected.
Crohn's disease Case GSM76072 Crohn's Disease subject (52 year old caucasian male, SAK_1280775705) PBMCs from Crohn's Disease subject None Case marker detected.
Crohn's disease Case GSM76073 Crohn's Disease subject (32 year old caucasian male, SAK_1287459252) PBMCs from Crohn's Disease subject None Case marker detected.
Crohn's disease Case GSM76074 Crohn's Disease subject (20 year old caucasian female, SAK_1287906498) PBMCs from Crohn's Disease subject None Case marker detected.
Crohn's disease Case GSM76075 Crohn's Disease subject (27 year old caucasian female, SAK_1275500386) PBMCs from Crohn's Disease subject None Case marker detected.
Crohn's disease Case GSM76076 Crohn's Disease subject (47 year old caucasian female, SAK_1263249533) PBMCs from Crohn's Disease subject None Case marker detected.
Crohn's disease Case GSM76077 Crohn's Disease subject (58 year old caucasian female, SAK_1275433327) PBMCs from Crohn's Disease subject None Case marker detected.
Crohn's disease Case GSM76078 Crohn's Disease subject (33 year old caucasian male, SAK_1260857762) PBMCs from Crohn's Disease subject None Case marker detected.
Crohn's disease Case GSM76079 Crohn's Disease subject (65 year old caucasian female, SAK_1280798058) PBMCs from Crohn's Disease subject None Case marker detected.
35 additional case samples are hidden from this preview.
Normal tissue Control GSM76115 Normal subject (60 year old caucasian male, SAK_1287302781) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76116 Normal subject (53 year old caucasian male, SAK_1287347487) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76117 Normal subject (54 year old caucasian male, SAK_1287392193) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76118 Normal subject (53 year old caucasian male, SAK_1288621868) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76119 Normal subject (54 year old caucasian female, SAK_1289203312) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76120 Normal subject (47 year old caucasian female, SAK_1289248024) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76121 Normal subject (48 year old caucasian female, SAK_1289292737) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76122 Normal subject (47 year old caucasian female, SAK_1289471570) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76123 Normal subject (42 year old caucasian female, SAK_1289918632) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76124 Normal subject (54 year old caucasian male, SAK_1289963270) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76125 Normal subject (56 year old caucasian female, SAK_1290052750) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76126 Normal subject (52 year old caucasian female, SAK_1290097388) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76127 Normal subject (45 year old caucasian female, SAK_1290231506) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76128 Normal subject (51 year old caucasian female, SAK_1290253859) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76129 Normal subject (57 year old caucasian male, SAK_1290276212) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76130 Normal subject (45 year old caucasian male, SAK_1290589154) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76131 Normal subject (36 year old caucasian male, SAK_1782763706) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76132 Normal subject (42 year old caucasian male, SAK_1274829796) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76133 Normal subject (35 year old caucasian female, SAK_1265842481) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76134 Normal subject (31 year old indian male, SAK_1274852149) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76135 Normal subject (31 year old caucasian female, SAK_1265864834) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76136 Normal subject (42 year old caucasian male, SAK_1782808510) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76137 Normal subject (54 year old caucasian female, SAK_1276103927) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76138 Normal subject (47 year old caucasian male, SAK_1274874502) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76139 Normal subject (49 year old caucasian male, SAK_1254531863) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76140 Normal subject (51 year old caucasian female, SAK_1276014509) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76141 Normal subject (28 year old caucasian female, SAK_1265909540) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76142 Normal subject (39 year old caucasian female, SAK_1265797775) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76143 Normal subject (31 year old asian male, SAK_1265931893) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76144 Normal subject (42 year old caucasian male, SAK_1265954246) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76145 Normal subject (44 year old caucasian female, SAK_1279948644) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76146 Normal subject (42 year old caucasian male, SAK_1254621275) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76147 Normal subject (33 year old caucasian male, SAK_1274807443) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76148 Normal subject (40 year old caucasian male, SAK_1254688334) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76149 Normal subject (42 year old caucasian male, SAK_1276036865) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76150 Normal subject (50 year old caucasian male, SAK_1276059218) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76151 Normal subject (47 year old caucasian male, SAK_1279993350) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76152 Normal subject (46 year old caucasian female, SAK_1280015703) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76153 Normal subject (40 year old caucasian male, SAK_1265998952) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76154 Normal subject (27 year old caucasian female, SAK_1276081571) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76155 Normal subject (25 year old caucasian male, SAK_1280038056) PBMCs from Normal subject None Control marker detected.
Normal tissue Control GSM76156 Normal subject (40 year old caucasian male, SAK_1265820128) PBMCs from Normal subject None 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.