GSE83448

Genome-wide transcriptional analysis in intestinal biopsies from Crohn's disease (CD) patients.

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

19 case / 34 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
53 samples
Specimen
Tissue
Reported/interpreted study design
Disease/model vs control Design classification does not establish patient pairs.
Comparison type
Tumor vs normal
Contributors
Josep M, Aterido A
Contact name
Adrià Aterido
Submission date
2016-06-16
Last update
2021-09-05
Organization
Vall d'Hebron Hospital Research Institute
Department
Rheumatology Research Group
Public date
2020-06-08
Experiment types
Expression profiling by array
Platforms
GPL18134 CodeLink Human Whole Genome Array [DISCOVERY probe type]
Series type
Series
SubSeries
Not available
BioProject
PRJNA326248

Summary

Differential gene expression analysis between CD patients and controls to identify the transcriptional signature that defines the inflamed intestinal mucosa in CD.

Overall design

Intestinal biopsy samples were obtained from CD patients and healthy controls. RNA was subsequently extracted from each sample. Gene expression intensities were measured using GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray. After performing the gene expression quality control analysis, we characterized the transcriptional profile of the inflamed intestinal mucosa in CD.

Source Evidence

4 sources
Source Contribution Status
GEO

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

Sample records
53 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.

3 linked publications 3 DOIs

Primary publication

  1. Transcriptomic identification of TMIGD1 and its relationship with the ileal epithelial cell differentiation in Crohn's disease. American journal of physiology. Gastrointestinal and liver physiology, 2020

Related publications

  1. S-palmitoylation-related genes in Crohn's disease: Bioinformatic identification and validation. Biomolecules & biomedicine, 2025
  2. Identification and validation of key long non-coding RNAs using co-expression network analysis in Crohn's disease. Annals of palliative medicine, 2021
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 Inflamed tissue 19 samples
  • Likely control group Mixed controls 34 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 3 publications; 3 DOIs available: PMID 32508154, PMID 34628888, PMID 41364644.
  • Publication context: Transcriptomic identification of TMIGD1 and its relationship with the ileal epithelial cell differentiation in Crohn's disease.. American journal of physiology. Gastrointestinal and liver physiology, 2020. PMID 32508154. DOI 10.1152/ajpgi.00027.2020.
  • Publication context: Identification and validation of key long non-coding RNAs using co-expression network analysis in Crohn's disease.. Annals of palliative medicine, 2021. PMID 34628888. DOI 10.21037/apm-21-1952.
  • Publication context: S-palmitoylation-related genes in Crohn's disease: Bioinformatic identification and validation.. Biomolecules & biomedicine, 2025. PMID 41364644. DOI 10.17305/bb.2025.13221.

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.
  • 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

149 fields

Sample Group Preview

53 rows shown Show Hide
Study totals: Case 19 | Control 34 | Unassigned 0 | Excluded 0 | Ambiguous 0 53 rows shown
Group Role Accession Title Source / characteristics Reason
Inflamed tissue Case GSM2203118 Crohn's_Disease__patient1 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Inflamed margin Case marker detected.
Inflamed tissue Case GSM2203119 Crohn's_Disease__patient2 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Inflamed margin Case marker detected.
Inflamed tissue Case GSM2203120 Crohn's_Disease__patient3 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Inflamed margin Case marker detected.
Inflamed tissue Case GSM2203122 Crohn's_Disease__patient4 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Inflamed margin Case marker detected.
Inflamed tissue Case GSM2203123 Crohn's_Disease__patient5 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Inflamed margin Case marker detected.
Inflamed tissue Case GSM2203124 Crohn's_Disease__patient6 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Inflamed margin Case marker detected.
Inflamed tissue Case GSM2203126 Crohn's_Disease__patient7 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Inflamed margin Case marker detected.
Inflamed tissue Case GSM2203127 Crohn's_Disease__patient8 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Inflamed margin Case marker detected.
Inflamed tissue Case GSM2203128 Crohn's_Disease__patient9 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Inflamed margin Case marker detected.
Inflamed tissue Case GSM2203130 Crohn's_Disease__patient10 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Inflamed margin Case marker detected.
Inflamed tissue Case GSM2203131 Crohn's_Disease__patient11 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Inflamed margin Case marker detected.
Inflamed tissue Case GSM2203133 Crohn's_Disease__patient12 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Inflamed margin Case marker detected.
Inflamed tissue Case GSM2203134 Crohn's_Disease__patient13 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Inflamed margin Case marker detected.
Inflamed tissue Case GSM2203135 Crohn's_Disease__patient14 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Inflamed margin Case marker detected.
Inflamed tissue Case GSM2203137 Crohn's_Disease__patient15 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Inflamed margin Case marker detected.
Inflamed tissue Case GSM2203138 Crohn's_Disease__patient16 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Inflamed margin Case marker detected.
Inflamed tissue Case GSM2203139 Crohn's_Disease__patient17 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Inflamed margin Case marker detected.
Inflamed tissue Case GSM2203142 Crohn's_Disease__patient18 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Inflamed margin Case marker detected.
Inflamed tissue Case GSM2203143 Crohn's_Disease__patient19 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Inflamed margin Case marker detected.
Healthy control Control GSM2203115 Healthy_control_subject1 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Control Sample-local control marker detected.
Healthy control Control GSM2203116 Healthy_control_subject2 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Control Sample-local control marker detected.
Healthy control Control GSM2203117 Healthy_control_subject3 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Control Sample-local control marker detected.
Healthy control Control GSM2203121 Healthy_control_subject4 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Control Sample-local control marker detected.
Healthy control Control GSM2203125 Healthy_control_subject5 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Control Sample-local control marker detected.
Healthy control Control GSM2203129 Healthy_control_subject6 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Control Sample-local control marker detected.
Healthy control Control GSM2203132 Healthy_control_subject7 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Control Sample-local control marker detected.
Healthy control Control GSM2203136 Healthy_control_subject8 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Control Sample-local control marker detected.
Healthy control Control GSM2203140 Healthy_control_subject9 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Control Sample-local control marker detected.
Healthy control Control GSM2203141 Healthy_control_subject10 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Control Sample-local control marker detected.
Healthy control Control GSM2203144 Healthy_control_subject11 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Control Sample-local control marker detected.
Healthy control Control GSM2203145 Healthy_control_subject12 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Control Sample-local control marker detected.
Healthy control Control GSM2203146 Healthy_control_subject13 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Control Sample-local control marker detected.
Healthy control Control GSM2203147 Healthy_control_subject14 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Control Sample-local control marker detected.
Non-inflamed tissue Control GSM2203148 Crohn's_Disease__patient20 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Non-inflamed margin Control marker detected.
Non-inflamed tissue Control GSM2203149 Crohn's_Disease__patient21 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Non-inflamed margin Control marker detected.
Non-inflamed tissue Control GSM2203150 Crohn's_Disease__patient22 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Non-inflamed margin Control marker detected.
Non-inflamed tissue Control GSM2203151 Crohn's_Disease__patient23 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Non-inflamed margin Control marker detected.
Non-inflamed tissue Control GSM2203152 Crohn's_Disease__patient24 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Non-inflamed margin Control marker detected.
Non-inflamed tissue Control GSM2203153 Crohn's_Disease__patient25 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Non-inflamed margin Control marker detected.
Non-inflamed tissue Control GSM2203154 Crohn's_Disease__patient26 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Non-inflamed margin Control marker detected.
Non-inflamed tissue Control GSM2203155 Crohn's_Disease__patient27 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Non-inflamed margin Control marker detected.
Non-inflamed tissue Control GSM2203156 Crohn's_Disease__patient28 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Non-inflamed margin Control marker detected.
Non-inflamed tissue Control GSM2203157 Crohn's_Disease__patient29 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Non-inflamed margin Control marker detected.
Non-inflamed tissue Control GSM2203158 Crohn's_Disease__patient30 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Non-inflamed margin Control marker detected.
Non-inflamed tissue Control GSM2203159 Crohn's_Disease__patient31 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Non-inflamed margin Control marker detected.
Non-inflamed tissue Control GSM2203160 Crohn's_Disease__patient32 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Non-inflamed margin Control marker detected.
Non-inflamed tissue Control GSM2203161 Crohn's_Disease__patient33 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Non-inflamed margin Control marker detected.
Non-inflamed tissue Control GSM2203162 Crohn's_Disease__patient34 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Non-inflamed margin Control marker detected.
Non-inflamed tissue Control GSM2203163 Crohn's_Disease__patient35 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Non-inflamed margin Control marker detected.
Non-inflamed tissue Control GSM2203164 Crohn's_Disease__patient36 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Non-inflamed margin Control marker detected.
Non-inflamed tissue Control GSM2203165 Crohn's_Disease__patient37 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Non-inflamed margin Control marker detected.
Non-inflamed tissue Control GSM2203166 Crohn's_Disease__patient38 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Non-inflamed margin Control marker detected.
Non-inflamed tissue Control GSM2203167 Crohn's_Disease__patient39 Intestinal mucosa Tissue: Intestinal mucosa; Inflammation: Non-inflamed margin 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.