GSE1141

Inflammatory bowel disease (HG-U133A)

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

4 case / 2 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: 6 samples
Specimen: Biopsy
Reported/interpreted study design: Disease/model vs control Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Langmann T, Moehle C, Mauerer R, Scharl M, Liebisch G, Zahn A, Stremmel W, Schmitz G
Contact name: Thomas Langmann
Submission date: 2004-03-24
Last update: 2018-08-10
Organization: Institute of Human Genetics
Department: University of Regensburg
Public date: 2004-04-20
Experiment types: Expression profiling by array
Platforms: GPL96 [HG-U133A] Affymetrix Human Genome U133A Array
Series type: Series
SubSeries: Not available
BioProject: PRJNA87261

Summary

Samples for microarray analysis were derived from terminal ileum and colonic tissues from probands with Crohn´s disease and Ulcerative Colitis and control patients, respectively. IBD tissue biopsies from non-inflamed regions 10 cm distant from pathological areas were selected. To minimize inter-individual differences in gene expression and to enrich for IBD-specific transcriptional events, 2.5 µg of total RNA from terminal ileum and colon transversum from four individuals of each patient and control group were used for pooling. Gene expression profiles were determined using Affymetrix HG-U133A Gene Chips. Keywords: ordered

Overall design

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 6 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, inflammatory bowel disease, ulcerative colitis Disease context came from Normalization rules.
Likely case group Crohn's disease 4 samples
Likely control group Control 2 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: Biopsy. Comparison suitability: 0%.
Interpreted disease metadata: Crohn's disease, Inflammatory bowel disease, Ulcerative colitis.
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.
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.
Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

Microarray expression context was detected; compare separately from RNA-seq cohorts.
Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.

Normalized Fields

39 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source ileum GSM19135 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ileum sample_title: IBD_Control Ileum (HG-U133A) sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM19137 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon sample_title: IBD_Control Colon (HG-U133A) sample-anatomical-source-v1 sample-local anatomical source

anatomical_source ileum GSM19138 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ileum sample_title: IBD_Crohn Ileum (HG-U133A) sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM19139 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon sample_title: IBD_Crohn Colon (HG-U133A) sample-anatomical-source-v1 sample-local anatomical source

anatomical_source ileum GSM19140 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ileum sample_title: IBD_Colitis Ileum (HG-U133A) sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM19141 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon sample_title: IBD_Colitis Colon (HG-U133A) sample-anatomical-source-v1 sample-local anatomical source

assay_type microarray GSE1141 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence microarray dataset_accession: GSE1141 dataset_title: Inflammatory bowel disease (HG-U133A) organism: Homo sapiens assay_type: microarray processed_data_available: true raw_data_available: ... keyword match keyword match: microarray

collection_method biopsy GSM19135 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy IBD_Control Ileum (HG-U133A) mucosal biopsy (pool of 4 different donors) none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM19137 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy IBD_Control Colon (HG-U133A) mucosal biopsy (pool of 4 different donors) none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM19138 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy IBD_Crohn Ileum (HG-U133A) mucosal biopsy (pool of 4 different donors) none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM19139 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy IBD_Crohn Colon (HG-U133A) mucosal biopsy (pool of 4 different donors) none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM19140 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy IBD_Colitis Ileum (HG-U133A) mucosal biopsy (pool of 4 different donors) none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM19141 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy IBD_Colitis Colon (HG-U133A) mucosal biopsy (pool of 4 different donors) none controlled vocabulary controlled vocabulary collection method match: biopsy

disease Crohn's disease GSE1141 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease dataset_accession: GSE1141 dataset_title: Inflammatory bowel disease (HG-U133A) organism: Homo sapiens assay_type: microarray processed_data_available: true raw_data_available: ... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease inflammatory bowel disease GSE1141 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflammatory bowel disease dataset_accession: GSE1141 dataset_title: Inflammatory bowel disease (HG-U133A) organism: Homo sapiens assay_type: microarray processed_data_available: true raw_data_available: ... controlled vocabulary controlled vocabulary disease match: inflammatory bowel disease

disease ulcerative colitis GSE1141 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis dataset_accession: GSE1141 dataset_title: Inflammatory bowel disease (HG-U133A) organism: Homo sapiens assay_type: microarray processed_data_available: true raw_data_available: ... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease inflammatory bowel disease GSM19135 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ibd IBD_Control Ileum (HG-U133A) mucosal biopsy (pool of 4 different donors) none controlled vocabulary controlled vocabulary disease match: ibd

disease inflammatory bowel disease GSM19137 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ibd IBD_Control Colon (HG-U133A) mucosal biopsy (pool of 4 different donors) none controlled vocabulary controlled vocabulary disease match: ibd

disease Crohn's disease GSM19138 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence Crohn IBD_Crohn Ileum (HG-U133A) mucosal biopsy (pool of 4 different donors) none controlled vocabulary controlled vocabulary disease match: Crohn

disease inflammatory bowel disease GSM19138 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ibd IBD_Crohn Ileum (HG-U133A) mucosal biopsy (pool of 4 different donors) none controlled vocabulary controlled vocabulary disease match: ibd

disease Crohn's disease GSM19139 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence Crohn IBD_Crohn Colon (HG-U133A) mucosal biopsy (pool of 4 different donors) none controlled vocabulary controlled vocabulary disease match: Crohn

disease inflammatory bowel disease GSM19139 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ibd IBD_Crohn Colon (HG-U133A) mucosal biopsy (pool of 4 different donors) none controlled vocabulary controlled vocabulary disease match: ibd

disease inflammatory bowel disease GSM19140 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ibd IBD_Colitis Ileum (HG-U133A) mucosal biopsy (pool of 4 different donors) none controlled vocabulary controlled vocabulary disease match: ibd

disease inflammatory bowel disease GSM19141 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ibd IBD_Colitis Colon (HG-U133A) mucosal biopsy (pool of 4 different donors) none controlled vocabulary controlled vocabulary disease match: ibd

organism Homo sapiens GSE1141 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE1141 dataset_title: Inflammatory bowel disease (HG-U133A) organism: Homo sapiens assay_type: microarray processed_data_available: true raw_data_available: ... keyword match keyword match: homo sapiens

primary_tissue primary tissue GSM19135 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy IBD_Control Ileum (HG-U133A) mucosal biopsy (pool of 4 different donors) none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM19137 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy IBD_Control Colon (HG-U133A) mucosal biopsy (pool of 4 different donors) none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM19138 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy IBD_Crohn Ileum (HG-U133A) mucosal biopsy (pool of 4 different donors) none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM19139 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy IBD_Crohn Colon (HG-U133A) mucosal biopsy (pool of 4 different donors) none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM19140 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy IBD_Colitis Ileum (HG-U133A) mucosal biopsy (pool of 4 different donors) none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM19141 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy IBD_Colitis Colon (HG-U133A) mucosal biopsy (pool of 4 different donors) none controlled vocabulary controlled vocabulary primary tissue match: biopsy

tissue colon GSE1141 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon dataset_accession: GSE1141 dataset_title: Inflammatory bowel disease (HG-U133A) organism: Homo sapiens assay_type: microarray processed_data_available: true raw_data_available: ... controlled vocabulary controlled vocabulary tissue match: colon

tissue intestine GSE1141 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ileum dataset_accession: GSE1141 dataset_title: Inflammatory bowel disease (HG-U133A) organism: Homo sapiens assay_type: microarray processed_data_available: true raw_data_available: ... controlled vocabulary controlled vocabulary tissue match: ileum

tissue intestine GSM19135 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ileum IBD_Control Ileum (HG-U133A) mucosal biopsy (pool of 4 different donors) none controlled vocabulary controlled vocabulary tissue match: ileum

tissue colon GSM19137 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon IBD_Control Colon (HG-U133A) mucosal biopsy (pool of 4 different donors) none controlled vocabulary controlled vocabulary tissue match: colon

tissue intestine GSM19138 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ileum IBD_Crohn Ileum (HG-U133A) mucosal biopsy (pool of 4 different donors) none controlled vocabulary controlled vocabulary tissue match: ileum

tissue colon GSM19139 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon IBD_Crohn Colon (HG-U133A) mucosal biopsy (pool of 4 different donors) none controlled vocabulary controlled vocabulary tissue match: colon

tissue intestine GSM19140 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ileum IBD_Colitis Ileum (HG-U133A) mucosal biopsy (pool of 4 different donors) none controlled vocabulary controlled vocabulary tissue match: ileum

tissue colon GSM19141 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon IBD_Colitis Colon (HG-U133A) mucosal biopsy (pool of 4 different donors) none controlled vocabulary controlled vocabulary tissue match: colon

Sample Group Preview

6 rows shown Show Hide

Study totals: Case 4 | Control 2 | Unassigned 0 | Excluded 0 | Ambiguous 0 6 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Crohn's disease	Case	GSM19138	IBD_Crohn Ileum (HG-U133A)	Mucosal biopsy (pool of 4 different donors) None	Case marker detected.
Crohn's disease	Case	GSM19139	IBD_Crohn Colon (HG-U133A)	Mucosal biopsy (pool of 4 different donors) None	Case marker detected.
Inflammatory bowel disease	Case	GSM19140	IBD_Colitis Ileum (HG-U133A)	Mucosal biopsy (pool of 4 different donors) None	Case marker detected.
Inflammatory bowel disease	Case	GSM19141	IBD_Colitis Colon (HG-U133A)	Mucosal biopsy (pool of 4 different donors) None	Case marker detected.
Control	Control	GSM19135	IBD_Control Ileum (HG-U133A)	Mucosal biopsy (pool of 4 different donors) None	Sample-local control marker detected.
Control	Control	GSM19137	IBD_Control Colon (HG-U133A)	Mucosal biopsy (pool of 4 different donors) None	Sample-local 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.