GSE46754

Gene expression analysis of omental and mesenteric adipose tissue in Crohn's disease and ulcerative colitis

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

8 case / 0 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
8 samples
Specimen
Tissue
Reported/interpreted study design
Unclear study design Design classification does not establish patient pairs.
Comparison type
Tumor vs normal
Contributors
Zulian A, Alessandra Z
Contact name
Zulian Alessandra
Submission date
2013-05-08
Last update
2019-10-24
Organization
istituto auxologico italiano
Department
Not available
Public date
2013-05-09
Experiment types
Expression profiling by array
Platforms
GPL6947 Illumina HumanHT-12 V3.0 expression beadchip
Series type
Series
SubSeries
Not available
BioProject
PRJNA202246

Summary

Our hypothesis is that in IBD patients intestinal bacteria translocation into the intra-abdominal fat depots affects adipocyte morphology and gene expression. The study aimed to study adipocyte gene expression of omental (OM) and mesenteric (MES) adipose tissue of ulcerative colitis (UC) and crohn's disease (CD).

Overall design

Total RNA was extracted from isolated adipocytes from omental and mesenteric adipose tissue of CD and UC patients. Microarray experiments were performed in duplicates of 4 different pools of RNAs extracted from adipocytes isolated from OM and MES of UC patients (n=5) and CD patients (n=5) respectively.

Source Evidence

4 sources
Source Contribution Status
GEO

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

Sample records
8 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. Differences in visceral fat and fat bacterial colonization between ulcerative colitis and Crohn's disease. An in vivo and in vitro study. PloS one, 2013
Available

Metadata Quality Components

Persisted metadata quality

93 pts
Clarity
93%
Weight
100 pts

Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Only one side of the comparison is clearly grouped. 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

Not ready
55% DE readiness

Contrast completeness

10/25 pts

Only one side of the contrast is present; downstream DE needs both groups.

Minimum group size

0/20 pts

Minimum group size cannot be evaluated until a complete contrast exists.

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

0/10 pts

Critical warnings must be resolved before downstream analysis.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

  • No complete case/control contrast is available.
  • Critical dataset warnings must be resolved.

Next Steps

  • Resolve critical warnings before downstream analysis.

Analysis Preparation Checklist

4/6 ready

Group labels reviewed

Blocked

No complete case/control grouping exists yet.

Review the sample grouping table and assign both case and control groups.

Minimum sample count met

Blocked

At least one group has fewer than 2 samples.

Choose a larger dataset or merge only scientifically valid groups.

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.

Analysis readiness has blockers that must be resolved before DE.

Analysis preparation checklist contains blocked items.

No complete case/control or treatment/control contrast is available.

At least one comparison group has fewer than two samples.

Critical dataset warnings are present.

Assay context may require expert handling before DESeq2-style analysis.

Study design is model-system or unclear and should be reviewed before 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 Crohn's disease 8 samples
  • Likely control group No control group detected 0 samples

Intent Interpretation

  • Downgrade or exclusion reason Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

  • 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 24205244.
  • Publication context: Differences in visceral fat and fat bacterial colonization between ulcerative colitis and Crohn's disease. An in vivo and in vitro study.. PloS one, 2013. PMID 24205244. DOI 10.1371/journal.pone.0078495.

Cautions

  • Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%.
  • Downgraded for tissue search because study design or specimen source is unclear.
  • Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
  • Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
  • Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
  • 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 fewer than ten samples limit cohort confidence.
  • Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
  • Missing or unclear metadata. Comparison - Unclear study design. Specimen - Tissue. Comparison suitability: 0%.
  • Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

Normalized Fields

14 fields

Sample Group Preview

8 rows shown Show Hide
Study totals: Case 8 | Control 0 | Unassigned 0 | Excluded 0 | Ambiguous 0 8 rows shown
Group Role Accession Title Source / characteristics Reason
Crohn's disease Case GSM1138177 CD OM_1 replicate Isolated adipocytes Tissue: Omental adipocytes from 5 patients pooled; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1138178 CD OM_2 replicate Isolated adipocytes Tissue: Omental adipocytes from 5 patients pooled; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1138179 CD MES_1 replicate Isolated adipocytes Tissue: Mesenteric adipocytes from 5 patients pooled; Disease state: Crohn's disease Case marker detected.
Crohn's disease Case GSM1138180 CD MES_2 replicate Isolated adipocytes Tissue: Mesenteric adipocytes from 5 patients pooled; Disease state: Crohn's disease Case marker detected.
Ulcerative colitis Case GSM1138181 UC OM_1 replicate Isolated adipocytes Tissue: Omental adipocytes from 5 patients pooled; Disease state: Ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM1138182 UC OM_2 replicate Isolated adipocytes Tissue: Omental adipocytes from 5 patients pooled; Disease state: Ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM1138183 UC MES_1 replicate Isolated adipocytes Tissue: Mesenteric adipocytes from 5 patients pooled; Disease state: Ulcerative colitis Case marker detected.
Ulcerative colitis Case GSM1138184 UC MES_2 replicate Isolated adipocytes Tissue: Mesenteric adipocytes from 5 patients pooled; Disease state: Ulcerative colitis Case 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.