GSE10791

Gene expression profiles in sigmoid colon biopsies from healthy and patients with 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

1 case / 1 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: 2 samples
Specimen: Biopsy
Reported/interpreted study design: Disease/model vs control Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Wu F, Kwon JH
Contact name: John H Kwon
Submission date: 2008-03-11
Last update: 2019-03-25
Organization: Johns Hopkins Univ
Department: Medicine
Public date: 2009-03-02
Experiment types: Expression profiling by array
Platforms: GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
Series type: Series
SubSeries: Not available
BioProject: PRJNA107485

Summary

Gene expression profiles were performed to compare the difference in sigmoid colon biopsies between from healthy control and patients with ulcerative colitis. Keywords: disease signature

Overall design

Total RNA was isolated sigmoid biopdy from 5 healthy and 6 UC patients. Pooled 5 ug total RNA equally for each group was used and followed the Affymetrix standard protocol for microarray.

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 2 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 MicroRNAs are differentially expressed in ulcerative colitis and alter expression of macrophage inflammatory peptide-2 alpha. Gastroenterology, 2008 PubMed DOI	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

Review before analysis

85% DE readiness

Contrast completeness

25/25 pts

Both case and control groups are present in the proposed grouping.

Minimum group size

8/20 pts

A contrast exists, but at least one group is below the minimum sample count.

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

At least one contrast group is below the minimum sample count.

Next Steps

Review blockers and update sample grouping or dataset selection before analysis.

Analysis Preparation Checklist

4/6 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

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.

At least one comparison group has fewer than two samples.

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 Ulcerative colitis Disease context came from Normalization rules.
Likely case group Ulcerative colitis 1 samples
Likely control group Healthy control 1 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: Ulcerative colitis.
Processed data is available for downstream review.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 18835392.
Publication context: MicroRNAs are differentially expressed in ulcerative colitis and alter expression of macrophage inflammatory peptide-2 alpha.. Gastroenterology, 2008. PMID 18835392. DOI 10.1053/j.gastro.2008.07.068.

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 six samples are too small for top-ranked 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

Total sample count is below the minimum needed for two comparison groups.
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

14 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source colon GSM272418 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM272419 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

assay_type microarray GSE10791 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence microarray dataset_accession: GSE10791 dataset_title: Gene expression profiles in sigmoid colon biopsies from healthy and patients with ulcerative colitis organism: Homo sapiens assay_type... keyword match keyword match: microarray

collection_method biopsy GSM272418 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Gene expression in colon from Healthy controls sigmoid colon biopsy sigmoid colon biopsy from 5 normal healthy individuals controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM272419 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy gene expression profile in sigmoid colon of UC patient sigmoid colon biopsy sigmoid colon biopsy from 6 patients with ulcerative colitis (UC). controlled vocabulary controlled vocabulary collection method match: biopsy

disease ulcerative colitis GSE10791 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis dataset_accession: GSE10791 dataset_title: Gene expression profiles in sigmoid colon biopsies from healthy and patients with ulcerative colitis organism: Homo sapiens assay_type... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM272419 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis gene expression profile in sigmoid colon of UC patient sigmoid colon biopsy sigmoid colon biopsy from 6 patients with ulcerative colitis (UC). controlled vocabulary controlled vocabulary disease match: ulcerative colitis

organism Homo sapiens GSE10791 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE10791 dataset_title: Gene expression profiles in sigmoid colon biopsies from healthy and patients with ulcerative colitis organism: Homo sapiens assay_type... keyword match keyword match: homo sapiens

primary_tissue primary tissue GSM272418 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Gene expression in colon from Healthy controls sigmoid colon biopsy sigmoid colon biopsy from 5 normal healthy individuals controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM272419 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy gene expression profile in sigmoid colon of UC patient sigmoid colon biopsy sigmoid colon biopsy from 6 patients with ulcerative colitis (UC). controlled vocabulary controlled vocabulary primary tissue match: biopsy

sample_type normal tissue GSM272418 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal Gene expression in colon from Healthy controls sigmoid colon biopsy sigmoid colon biopsy from 5 normal healthy individuals controlled vocabulary controlled vocabulary sample type match: normal

tissue colon GSE10791 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon dataset_accession: GSE10791 dataset_title: Gene expression profiles in sigmoid colon biopsies from healthy and patients with ulcerative colitis organism: Homo sapiens assay_type... controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM272418 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Gene expression in colon from Healthy controls sigmoid colon biopsy sigmoid colon biopsy from 5 normal healthy individuals controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM272419 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon gene expression profile in sigmoid colon of UC patient sigmoid colon biopsy sigmoid colon biopsy from 6 patients with ulcerative colitis (UC). controlled vocabulary controlled vocabulary tissue match: colon

Sample Group Preview

2 rows shown Show Hide

Study totals: Case 1 | Control 1 | Unassigned 0 | Excluded 0 | Ambiguous 0 2 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Ulcerative colitis	Case	GSM272419	Gene expression profile in sigmoid colon of UC patient	Sigmoid colon biopsy Sigmoid colon biopsy from 6 patients with ulcerative colitis (UC).	Case marker detected.
Healthy control	Control	GSM272418	Gene expression in colon from Healthy controls	Sigmoid colon biopsy Sigmoid colon biopsy from 5 normal healthy individuals	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.

Summary

Overall design

Source Evidence

Primary publication

Metadata Quality Components

Analysis Readiness

Blockers

Next Steps

Analysis Preparation Checklist

Bioinformatician Review

Why This Is Ranked Here

Applied Review Decisions

Derived Classifications

Intent Interpretation

Ranking Facts

Supporting evidence

Cautions

Dataset Warnings

Normalized Fields

Sample Group Preview

Use as Discovery Cohort