Gene expression analysis in mesenteric arteries and veins in Crohn's disease compared to controls from nonIBD samples

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

15 case / 11 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: 26 samples
Specimen: Tissue
Reported/interpreted study design: Disease/model vs control Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Randolph GJ, Randolph G
Contact name: Gwendalyn Randolph
Submission date: 2015-03-05
Last update: 2019-01-23
Organization: Washington University School of Medicine
Department: Pathology and Immunology
Public date: 2015-03-05
Experiment types: Expression profiling by array
Platforms: GPL6480 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Probe Name version)
Series type: Series
SubSeries: Not available
BioProject: PRJNA277303

Summary

Histology in the mesentery pointed to altered blood vessels. This experiment was designed to define the differences in gene expression in vessels from Crohn's disease versus controls. Crohn's disease was separately evaluated in inflamed (central disease) areas and in adjacent noninflamed areas.

Overall design

Laser capture microdissection was carried out on Carnoy's fixed mesenteric samples, comparing normal arteries or veins with Crohn's inflamed or nonifnlamed arteries or veins.

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 26 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	Publication context when PubMed identifiers are already known.	No match found

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 15 samples
Likely control group Normal tissue 11 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.

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

Microarray expression context was detected; compare separately from RNA-seq cohorts.
Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.

Normalized Fields

30 fields

Field Value Source Derived by Confidence Evidence Reason

assay_type microarray GSE66545 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence microarray dataset_accession: GSE66545 dataset_title: Gene expression analysis in mesenteric arteries and veins in Crohn's disease compared to controls from nonIBD samples organism: Homo s... keyword match keyword match: microarray

disease Crohn's disease GSE66545 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease dataset_accession: GSE66545 dataset_title: Gene expression analysis in mesenteric arteries and veins in Crohn's disease compared to controls from nonIBD samples organism: Homo s... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM1624725 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence Crohn's crohn's artery1 artery from Crohn's mesenteric fat tissue: mesenteric fat; sample type: artery; disease state: Crohn's controlled vocabulary controlled vocabulary disease match: Crohn's

disease Crohn's disease GSM1624726 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence Crohn's crohn's vein1 vein from Crohn's mesenteric fat tissue: mesenteric fat; sample type: vein; disease state: Crohn's controlled vocabulary controlled vocabulary disease match: Crohn's

disease Crohn's disease GSM1624728 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence Crohn's crohn's artery2 artery from Crohn's mesenteric fat tissue: mesenteric fat; sample type: artery; disease state: Crohn's controlled vocabulary controlled vocabulary disease match: Crohn's

disease Crohn's disease GSM1624730 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence Crohn's crohn's artery3 artery from Crohn's mesenteric fat tissue: mesenteric fat; sample type: artery; disease state: Crohn's controlled vocabulary controlled vocabulary disease match: Crohn's

disease Crohn's disease GSM1624732 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence Crohn's crohn's vein2 vein from Crohn's mesenteric fat tissue: mesenteric fat; sample type: vein; disease state: Crohn's controlled vocabulary controlled vocabulary disease match: Crohn's

disease Crohn's disease GSM1624733 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence Crohn's crohn's vein3 vein from Crohn's mesenteric fat tissue: mesenteric fat; sample type: vein; disease state: Crohn's controlled vocabulary controlled vocabulary disease match: Crohn's

disease Crohn's disease GSM1624734 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence Crohn's crohn's artery4 artery from Crohn's mesenteric fat tissue: mesenteric fat; sample type: artery; disease state: Crohn's controlled vocabulary controlled vocabulary disease match: Crohn's

disease Crohn's disease GSM1624736 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence Crohn's crohn's vein4 vein from Crohn's mesenteric fat tissue: mesenteric fat; sample type: vein; disease state: Crohn's controlled vocabulary controlled vocabulary disease match: Crohn's

disease Crohn's disease GSM1624737 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence Crohn's crohn's vein5 vein from Crohn's mesenteric fat tissue: mesenteric fat; sample type: vein; disease state: Crohn's controlled vocabulary controlled vocabulary disease match: Crohn's

disease Crohn's disease GSM1624739 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence Crohn's crohn's artery5 artery from Crohn's mesenteric fat tissue: mesenteric fat; sample type: artery; disease state: Crohn's controlled vocabulary controlled vocabulary disease match: Crohn's

disease Crohn's disease GSM1624742 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence Crohn's crohn's artery6 artery from Crohn's mesenteric fat tissue: mesenteric fat; sample type: artery; disease state: Crohn's controlled vocabulary controlled vocabulary disease match: Crohn's

disease Crohn's disease GSM1624743 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence Crohn's crohn's vein6 vein from Crohn's mesenteric fat tissue: mesenteric fat; sample type: vein; disease state: Crohn's controlled vocabulary controlled vocabulary disease match: Crohn's

disease Crohn's disease GSM1624744 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence Crohn's crohn's vein7 vein from Crohn's mesenteric fat tissue: mesenteric fat; sample type: vein; disease state: Crohn's controlled vocabulary controlled vocabulary disease match: Crohn's

disease Crohn's disease GSM1624748 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence Crohn's crohn's vein8 vein from Crohn's mesenteric fat tissue: mesenteric fat; sample type: vein; disease state: Crohn's controlled vocabulary controlled vocabulary disease match: Crohn's

disease Crohn's disease GSM1624750 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence Crohn's crohn's vein9 vein from Crohn's mesenteric fat tissue: mesenteric fat; sample type: vein; disease state: Crohn's controlled vocabulary controlled vocabulary disease match: Crohn's

organism Homo sapiens GSE66545 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE66545 dataset_title: Gene expression analysis in mesenteric arteries and veins in Crohn's disease compared to controls from nonIBD samples organism: Homo s... keyword match keyword match: homo sapiens

sample_type normal tissue GSM1624727 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal normal vein1 vein from nonIBD mesenteric fat tissue: mesenteric fat; sample type: vein; disease state: nonIBD controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM1624729 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal normal artery1 artery from nonIBD mesenteric fat tissue: mesenteric fat; sample type: artery; disease state: nonIBD controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM1624731 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal normal artery2 artery from nonIBD mesenteric fat tissue: mesenteric fat; sample type: artery; disease state: nonIBD controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM1624735 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal normal vein2 vein from nonIBD mesenteric fat tissue: mesenteric fat; sample type: vein; disease state: nonIBD controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM1624738 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal normal vein3 vein from nonIBD mesenteric fat tissue: mesenteric fat; sample type: vein; disease state: nonIBD controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM1624740 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal normal vein4 vein from nonIBD mesenteric fat tissue: mesenteric fat; sample type: vein; disease state: nonIBD controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM1624741 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal normal artery3 artery from nonIBD mesenteric fat tissue: mesenteric fat; sample type: artery; disease state: nonIBD controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM1624745 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal normal artery4 artery from nonIBD mesenteric fat tissue: mesenteric fat; sample type: artery; disease state: nonIBD controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM1624746 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal normal artery5 artery from nonIBD mesenteric fat tissue: mesenteric fat; sample type: artery; disease state: nonIBD controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM1624747 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal normal vein5 vein from nonIBD mesenteric fat tissue: mesenteric fat; sample type: vein; disease state: nonIBD controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM1624749 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal normal vein6 vein from nonIBD mesenteric fat tissue: mesenteric fat; sample type: vein; disease state: nonIBD controlled vocabulary controlled vocabulary sample type match: normal

tissue blood GSE66545 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood dataset_accession: GSE66545 dataset_title: Gene expression analysis in mesenteric arteries and veins in Crohn's disease compared to controls from nonIBD samples organism: Homo s... controlled vocabulary controlled vocabulary tissue match: blood

Sample Group Preview

26 rows shown Show Hide

Study totals: Case 15 | Control 11 | Unassigned 0 | Excluded 0 | Ambiguous 0 26 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Crohn's disease	Case	GSM1624725	Crohn's artery1	Artery from Crohn's mesenteric fat Tissue: Mesenteric fat; Sample type: Artery; Disease state: Crohn's	Case marker detected.
Crohn's disease	Case	GSM1624726	Crohn's vein1	Vein from Crohn's mesenteric fat Tissue: Mesenteric fat; Sample type: Vein; Disease state: Crohn's	Case marker detected.
Crohn's disease	Case	GSM1624728	Crohn's artery2	Artery from Crohn's mesenteric fat Tissue: Mesenteric fat; Sample type: Artery; Disease state: Crohn's	Case marker detected.
Crohn's disease	Case	GSM1624730	Crohn's artery3	Artery from Crohn's mesenteric fat Tissue: Mesenteric fat; Sample type: Artery; Disease state: Crohn's	Case marker detected.
Crohn's disease	Case	GSM1624732	Crohn's vein2	Vein from Crohn's mesenteric fat Tissue: Mesenteric fat; Sample type: Vein; Disease state: Crohn's	Case marker detected.
Crohn's disease	Case	GSM1624733	Crohn's vein3	Vein from Crohn's mesenteric fat Tissue: Mesenteric fat; Sample type: Vein; Disease state: Crohn's	Case marker detected.
Crohn's disease	Case	GSM1624734	Crohn's artery4	Artery from Crohn's mesenteric fat Tissue: Mesenteric fat; Sample type: Artery; Disease state: Crohn's	Case marker detected.
Crohn's disease	Case	GSM1624736	Crohn's vein4	Vein from Crohn's mesenteric fat Tissue: Mesenteric fat; Sample type: Vein; Disease state: Crohn's	Case marker detected.
Crohn's disease	Case	GSM1624737	Crohn's vein5	Vein from Crohn's mesenteric fat Tissue: Mesenteric fat; Sample type: Vein; Disease state: Crohn's	Case marker detected.
Crohn's disease	Case	GSM1624739	Crohn's artery5	Artery from Crohn's mesenteric fat Tissue: Mesenteric fat; Sample type: Artery; Disease state: Crohn's	Case marker detected.
Crohn's disease	Case	GSM1624742	Crohn's artery6	Artery from Crohn's mesenteric fat Tissue: Mesenteric fat; Sample type: Artery; Disease state: Crohn's	Case marker detected.
Crohn's disease	Case	GSM1624743	Crohn's vein6	Vein from Crohn's mesenteric fat Tissue: Mesenteric fat; Sample type: Vein; Disease state: Crohn's	Case marker detected.
Crohn's disease	Case	GSM1624744	Crohn's vein7	Vein from Crohn's mesenteric fat Tissue: Mesenteric fat; Sample type: Vein; Disease state: Crohn's	Case marker detected.
Crohn's disease	Case	GSM1624748	Crohn's vein8	Vein from Crohn's mesenteric fat Tissue: Mesenteric fat; Sample type: Vein; Disease state: Crohn's	Case marker detected.
Crohn's disease	Case	GSM1624750	Crohn's vein9	Vein from Crohn's mesenteric fat Tissue: Mesenteric fat; Sample type: Vein; Disease state: Crohn's	Case marker detected.
Normal tissue	Control	GSM1624727	Normal vein1	Vein from nonIBD mesenteric fat Tissue: Mesenteric fat; Sample type: Vein; Disease state: NonIBD	Control marker detected.
Normal tissue	Control	GSM1624729	Normal artery1	Artery from nonIBD mesenteric fat Tissue: Mesenteric fat; Sample type: Artery; Disease state: NonIBD	Control marker detected.
Normal tissue	Control	GSM1624731	Normal artery2	Artery from nonIBD mesenteric fat Tissue: Mesenteric fat; Sample type: Artery; Disease state: NonIBD	Control marker detected.
Normal tissue	Control	GSM1624735	Normal vein2	Vein from nonIBD mesenteric fat Tissue: Mesenteric fat; Sample type: Vein; Disease state: NonIBD	Control marker detected.
Normal tissue	Control	GSM1624738	Normal vein3	Vein from nonIBD mesenteric fat Tissue: Mesenteric fat; Sample type: Vein; Disease state: NonIBD	Control marker detected.
Normal tissue	Control	GSM1624740	Normal vein4	Vein from nonIBD mesenteric fat Tissue: Mesenteric fat; Sample type: Vein; Disease state: NonIBD	Control marker detected.
Normal tissue	Control	GSM1624741	Normal artery3	Artery from nonIBD mesenteric fat Tissue: Mesenteric fat; Sample type: Artery; Disease state: NonIBD	Control marker detected.
Normal tissue	Control	GSM1624745	Normal artery4	Artery from nonIBD mesenteric fat Tissue: Mesenteric fat; Sample type: Artery; Disease state: NonIBD	Control marker detected.
Normal tissue	Control	GSM1624746	Normal artery5	Artery from nonIBD mesenteric fat Tissue: Mesenteric fat; Sample type: Artery; Disease state: NonIBD	Control marker detected.
Normal tissue	Control	GSM1624747	Normal vein5	Vein from nonIBD mesenteric fat Tissue: Mesenteric fat; Sample type: Vein; Disease state: NonIBD	Control marker detected.
Normal tissue	Control	GSM1624749	Normal vein6	Vein from nonIBD mesenteric fat Tissue: Mesenteric fat; Sample type: Vein; Disease state: NonIBD	Control marker detected.

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Carry Siftome's disease, organism, specimen, assay, data type, and accession into a validation project. Uncertain fields remain Unknown.