GSE17594

NOD2 and human ileal gene expression

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 / 4 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
20 samples
Specimen
Tissue
Reported/interpreted study design
Disease/model vs control Design classification does not establish patient pairs.
Comparison type
Tumor vs normal
Contributors
Li E, Hunt S, Meyer R
Contact name
Rekha Meyer
Submission date
2009-08-11
Last update
2018-02-22
Organization
Washington University School of Medicine
Department
Not available
Public date
2010-01-01
Experiment types
Expression profiling by array
Platforms
GPL4133 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Feature Number version); GPL6848 Agilent-012391 Whole Human Genome Oligo Microarray G4112A (Probe Name version)
Series type
Series
SubSeries
Not available
BioProject
PRJNA118503

Summary

Profiling of ileal mucosal gene expression in Chron's disease patients with and without NOD2 risk alleles; through microarray analyses it was discovered that 18 genes related to lymphocyte and phagocyte activation recuitment were upregulated in affected ileum in NOD2R patients as compared to ileum in NOD2s (no risk alleles) patients, thus supporting the concept that NOD2 risk alleles contribute to impaired regulation of inflammation in the ileum.

Overall design

Mucosal biopsies of resected ileum were collected from 8 Crohn's disease patients at risk for NOD2R alleles. The patients were genotyped for the three major NOD2 risk alleles (Arg702Trp, Gly908Arg, Leu1007fs). Microarray analysis was performed in samples from NOD2R (at least one risk allele) Crohn’s disease patients, NOD2S (no risk alleles) Crohn’s disease patients and NOD2S controls.

Source Evidence

4 sources
Source Contribution Status
GEO

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

Sample records
20 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.

1 linked publication 1 DOI

Primary publication

  1. NOD2 status and human ileal gene expression. Inflammatory bowel diseases, 2010
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 Crohn's disease Disease context came from Normalization rules.
  • Likely case group Crohn's disease 16 samples
  • Likely control group Control 4 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: Crohn's disease.
  • Processed data is available for downstream review.
  • External evidence: PubMed links 1 publication; 1 DOI available: PMID 20155851.
  • Publication context: NOD2 status and human ileal gene expression.. Inflammatory bowel diseases, 2010. PMID 20155851. DOI 10.1002/ibd.21208.

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

66 fields

Sample Group Preview

20 rows shown Show Hide
Study totals: Case 16 | Control 4 | Unassigned 0 | Excluded 0 | Ambiguous 0 20 rows shown
Group Role Accession Title Source / characteristics Reason
Crohn's disease Case GSM438281 Unaffected ileum subject CD-124 N1 Macroscopic disease unaffected ileum, resection specimen from initial Ileocolic resection Nod2 genotype: WT/WT; Nod2 risk alleles (r = risk allele, nr= not risk allele): NOD2nr; Smoking history: No smoking history prior; Tnf infusion: Single anti-TNF infusion 18 months prior; Disease state: Crohn's disease; Tissue: Unaffected ileum Case marker detected.
Crohn's disease Case GSM438282 Affected ileum subject CD-124 II Macroscopic disease affected ileum, resection specimen from initial ileocolic resection Nod2 genotype: WT/WT; Nod2 risk alleles (r = risk allele, nr= not risk allele): NOD2nr; Smoking history: No smoking history prior; Tnf infusion: Single anti-TNF infusion 18 months prior; Disease state: Crohn's disease; Tissue: Affected ileum Case marker detected.
Crohn's disease Case GSM438283 Affected ileum subject CD-15 II Macroscopic disease affected ileum, resection specimen from initial ileocolic resection Nod2 genotype: R702W/WT; Nod2 risk alleles (r = risk allele, nr= not risk allele): NOD2r (1 allele); Smoking history: No smoking history prior; Tnf infusion: No anti TNF medication history prior; Disease state: Crohn's disease; Tissue: Affected ileum Case marker detected.
Crohn's disease Case GSM438284 Unaffected ileum subject CD-15 NI Macroscopic disease unaffected ileum, resection specimen from initial ileocolic resection Nod2 genotype: R702W/WT; Nod2 risk alleles (r = risk allele, nr= not risk allele): NOD2r (1 allele); Smoking history: No smoking history prior; Tnf infusion: No anti TNF medication history prior; Disease state: Crohn's disease; Tissue: Unaffected ileum Case marker detected.
Crohn's disease Case GSM438285 Unaffected ileum subject CD-19 NI Macroscopic disease unaffected ileum, resection specimen from initial ileocolic resection Nod2 genotype: WT/WT; Nod2 risk alleles (r = risk allele, nr= not risk allele): NOD2nr; Smoking history: No smoking history prior; Tnf infusion: No anti-TNF medication history prior; Disease state: Crohn's disease; Tissue: Unaffected ileum Case marker detected.
Crohn's disease Case GSM438286 Affected ileum subject CD-19 II Macroscopic disease affected ileum, resection specimen from initial ileocolic resection Nod2 genotype: WT/WT; Nod2 risk alleles (r = risk allele, nr= not risk allele): NOD2nr; Smoking history: No smoking history prior; Tnf infusion: No anti-TNF medication history prior; Disease state: Crohn's disease; Tissue: Affected ileum Case marker detected.
Crohn's disease Case GSM438287 Unaffected ileum subject CD-196 NI Macroscopic disease unaffected ileum, specimen from initial ileocolic resection Nod2 genotype: InsC/R702W; Nod2 risk alleles (r = risk allele, nr= not risk allele): NOD2r (2 allele); Smoking history: No smoking history prior; Tnf infusion: No anti TNF medication history prior; Disease state: Crohn's disease; Tissue: Unaffected ileum Case marker detected.
Crohn's disease Case GSM438288 Affected ileum subject CD-196 II Macroscopic disease affected ileum, specimen from initial ileocolic resection Nod2 genotype: InsC/R702W; Nod2 risk alleles (r = risk allele, nr= not risk allele): NOD2r (2 allele); Smoking history: No smoking history prior; Tnf infusion: No anti TNF medication history prior; Disease state: Crohn's disease; Tissue: Affected ileum Case marker detected.
Crohn's disease Case GSM438289 Affected ileum subject CD-22 II Macroscopic disease affected ileum, specimen from initial ileocolic resection Nod2 genotype: WT/WT; Nod2 risk alleles (r = risk allele, nr= not risk allele): NOD2nr; Smoking history: No smoking history prior; Tnf infusion: No anti-TNF medication history prior; Disease state: Crohn's disease; Tissue: Affected ileum Case marker detected.
Crohn's disease Case GSM438290 Unaffected ileum subject CD-22 NI Macroscopic disease unaffected ileum, specimen from initial ileocolic resection Nod2 genotype: WT/WT; Nod2 risk alleles (r = risk allele, nr= not risk allele): NOD2nr; Smoking history: No smoking history prior; Tnf infusion: No anti-TNF medication history prior; Disease state: Crohn's disease; Tissue: Unaffected ileum Case marker detected.
Crohn's disease Case GSM438291 Unaffected ileum subject CD-235 NI Macroscopic disease unaffected ileum, specimen from initial ileocolic resection Nod2 genotype: R702W/WT; Nod2 risk alleles (r = risk allele, nr= not risk allele): NOD2r (1 allele); Smoking history: No smoking history prior; Tnf infusion: No anti TNF medication history prior; Disease state: Crohn's disease; Tissue: Unaffected ileum Case marker detected.
Crohn's disease Case GSM438292 Affected ileum subject CD-235 II Macroscopic disease affected ileum, specimen from initial ileocolic resection Nod2 genotype: R702W/WT; Nod2 risk alleles (r = risk allele, nr= not risk allele): NOD2r (1 allele); Smoking history: No smoking history prior; Tnf infusion: No anti TNF medication history prior; Disease state: Crohn's disease; Tissue: Affected ileum Case marker detected.
Crohn's disease Case GSM438293 Unaffected ileum subject CD-256 NI Macroscopic disease unaffected ileum, specimen from initial ileocolic resection. Nod2 genotype: WT/WT; Nod2 risk alleles (r = risk allele, nr= not risk allele): NOD2nr; Smoking history: No smoking history prior; Tnf infusion: No anti-TNF medication history prior; Disease state: Crohn's disease; Tissue: Unaffected ileum Case marker detected.
Crohn's disease Case GSM438294 Affected ileum subject CD-256 II Macroscopic disease affected ileum, specimen from initial ileocolic resection Nod2 genotype: WT/WT; Nod2 risk alleles (r = risk allele, nr= not risk allele): NOD2nr; Smoking history: No smoking history prior; Tnf infusion: No anti-TNF medication history prior; Disease state: Crohn's disease; Tissue: Affected ileum Case marker detected.
Crohn's disease Case GSM438295 Unaffected ileum subject CD-312 NI Macroscopic disease unaffected ileum, specimen from initial ileocolic resection Nod2 genotype: InsC/InsC; Nod2 risk alleles (r = risk allele, nr= not risk allele): NOD2r; Smoking history: No smoking history prior; Tnf infusion: No anti-TNF medication history prior; Disease state: Crohn's disease; Tissue: Unaffected ileum Case marker detected.
Crohn's disease Case GSM438296 Affected ileum subject CD-312 II Macroscopic disease affected ileum, specimen from initial ileocolic resection Nod2 genotype: InsC/InsC; Nod2 risk alleles (r = risk allele, nr= not risk allele): NOD2r; Smoking history: No smoking history prior; Tnf infusion: No anti-TNF medication history prior; Disease state: Crohn's disease; Tissue: Affected ileum Case marker detected.
Control Control GSM438297 Unaffected ileum subject N13 NI Macroscopic disease unaffected ileum, specimen from initial total colectomy Nod2 genotype: WT/WT; Nod2 risk alleles (r = risk allele, nr= not risk allele): NOD2nr control patient; Smoking history: No smoking history prior; Tnf infusion: No anti-TNF medication history prior; Disease state: Control; Tissue: Unaffected ileum Sample-local control marker detected.
Control Control GSM438298 Unaffected ileum subject N15 NI Macroscopic disease unaffected ileum, specimen from initial right colectomy Nod2 genotype: WT/WT; Nod2 risk alleles (r = risk allele, nr= not risk allele): NOD2nr control patient; Smoking history: No smoking history prior; Tnf infusion: No anti-TNF medication history prior; Disease state: Control; Tissue: Unaffected ileum Sample-local control marker detected.
Control Control GSM438299 Unaffected ileum subject N33 NI Macroscopic disease unaffected ileum, specimen from initial total colectomy Nod2 genotype: WT/WT; Nod2 risk alleles (r = risk allele, nr= not risk allele): NOD2nr control patient; Smoking history: No smoking history prior; Tnf infusion: No anti-TNF medication history prior; Disease state: Control; Tissue: Unaffected ileum Sample-local control marker detected.
Control Control GSM438300 Unaffected ileum subject N34 NI Macroscopic disease unaffected ileum, specimen from initial total colectomy Nod2 genotype: WT/WT; Nod2 risk alleles (r = risk allele, nr= not risk allele): NOD2nr control patient; Smoking history: No smoking history prior; Tnf infusion: No anti-TNF medication history prior; Disease state: Control; Tissue: Unaffected ileum Sample-local control marker detected.

Use as Discovery Cohort

External Validation Finder

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