GSE26305

Genome-wide gene expression analysis for target genes to differentiate patients with intestinal tuberculosis and Crohn’s disease

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: Ahuja V, Subodh S, Tuteja A, Tiwari V, Kumar S, Narayanasamy K, Makharia G, Acharya SK
Contact name: Vineet Ahuja
Submission date: 2010-12-27
Last update: 2019-02-18
Organization: AIIMS
Department: Not available
Public date: 2011-01-04
Experiment types: Expression profiling by array
Platforms: GPL6884 Illumina HumanWG-6 v3.0 expression beadchip
Series type: Series
SubSeries: Not available
BioProject: PRJNA135119

Summary

This study aimed at genome-wide gene expression analysis of colonic biopsies from confirmed cases of intestinal tuberculosis (ITB) and Crohn's disease (CD) in comparison to controls. Further, to evaluate the role of T regulatory cells, Foxp3 mRNA expression was quantified in serum as well as colonic biopsies of patients with intestinal tuberculosis, Crohn's disease and controls.

Overall design

Paired samples, i.e. serum and colonic biopsies, were taken from 33 study subjects, which included patients with ITB and CD, and controls. RNA extraction was done and stringent quality checks performed. Human whole genome gene expression microarray analysis was performed on the Illumina HumanWG-6 Bead Chip with six total RNA samples of the 3 groups in duplicates. Real-time PCR for FOXP3 mRNA expression was analyzed in serum samples (4-CD, 5-ITB, 4-controls) and colonic biopsy samples (4-CD, 5-ITB, 4-controls).

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	Primary GEO citations and related PubMed articles that mention this dataset. 1 linked publication 1 DOI Primary publication Genome-wide gene expression analysis for target genes to differentiate patients with intestinal tuberculosis and Crohn's disease and discriminative value of FOXP3 mRNA expression. Gastroenterology report, 2016 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

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, tuberculosis 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, Tuberculosis.
Processed data is available for downstream review.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 25969456.
Publication context: Genome-wide gene expression analysis for target genes to differentiate patients with intestinal tuberculosis and Crohn's disease and discriminative value of FOXP3 mRNA expression.. Gastroenterology report, 2016. PMID 25969456. DOI 10.1093/gastro/gov015.

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.
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

36 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source colon GSM645979 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colonic tissue: colonic biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM646008 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colonic tissue: colonic biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM646009 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colonic tissue: colonic biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM646010 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colonic tissue: colonic biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM646011 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colonic tissue: colonic biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM646012 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colonic tissue: colonic biopsy sample-anatomical-source-v1 sample-local anatomical source

assay_type microarray GSE26305 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence microarray dataset_accession: GSE26305 dataset_title: Genome-wide gene expression analysis for target genes to differentiate patients with intestinal tuberculosis and Crohn’s disease organ... keyword match keyword match: microarray

collection_method biopsy GSM645979 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Biopsy_Control_015 Colonic biopsies, control age: 23 years; gender: male; sample type: control; tissue: colonic biopsy controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM646008 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Biopsy_Control_030 Colonic biopsies, control age: 65 years; gender: female; sample type: control; tissue: colonic biopsy controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM646009 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Biopsy_CD_017 Colonic biopsies, Crohn's disease age: 29 years; gender: male; disease state: Crohn's disease; tissue: colonic biopsy controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM646010 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Biopsy_CD_024 Colonic biopsies, Crohn's disease age: 40 years; gender: male; disease state: Crohn's disease; tissue: colonic biopsy controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM646011 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Biopsy_ITB_012 Colonic biopsies, intestinal tuberculosis disease age: 26 years; gender: female; disease state: intestinal tuberculosis disease; tissue: colonic biopsy controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM646012 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Biopsy_ITB_026 Colonic biopsies, intestinal tuberculosis disease age: 40 years; gender: female; disease state: intestinal tuberculosis disease; tissue: colonic biopsy controlled vocabulary controlled vocabulary collection method match: biopsy

disease Crohn's disease GSE26305 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease dataset_accession: GSE26305 dataset_title: Genome-wide gene expression analysis for target genes to differentiate patients with intestinal tuberculosis and Crohn’s disease organ... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease tuberculosis GSE26305 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence tuberculosis dataset_accession: GSE26305 dataset_title: Genome-wide gene expression analysis for target genes to differentiate patients with intestinal tuberculosis and Crohn’s disease organ... controlled vocabulary controlled vocabulary disease match: tuberculosis

disease Crohn's disease GSM646009 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Biopsy_CD_017 Colonic biopsies, Crohn's disease age: 29 years; gender: male; disease state: Crohn's disease; tissue: colonic biopsy controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM646010 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease Biopsy_CD_024 Colonic biopsies, Crohn's disease age: 40 years; gender: male; disease state: Crohn's disease; tissue: colonic biopsy controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease tuberculosis GSM646011 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence tuberculosis Biopsy_ITB_012 Colonic biopsies, intestinal tuberculosis disease age: 26 years; gender: female; disease state: intestinal tuberculosis disease; tissue: colonic biopsy controlled vocabulary controlled vocabulary disease match: tuberculosis

disease tuberculosis GSM646012 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence tuberculosis Biopsy_ITB_026 Colonic biopsies, intestinal tuberculosis disease age: 40 years; gender: female; disease state: intestinal tuberculosis disease; tissue: colonic biopsy controlled vocabulary controlled vocabulary disease match: tuberculosis

organism Homo sapiens GSE26305 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE26305 dataset_title: Genome-wide gene expression analysis for target genes to differentiate patients with intestinal tuberculosis and Crohn’s disease organ... keyword match keyword match: homo sapiens

primary_tissue primary tissue GSM645979 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Biopsy_Control_015 Colonic biopsies, control age: 23 years; gender: male; sample type: control; tissue: colonic biopsy controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM646008 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Biopsy_Control_030 Colonic biopsies, control age: 65 years; gender: female; sample type: control; tissue: colonic biopsy controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM646009 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Biopsy_CD_017 Colonic biopsies, Crohn's disease age: 29 years; gender: male; disease state: Crohn's disease; tissue: colonic biopsy controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM646010 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Biopsy_CD_024 Colonic biopsies, Crohn's disease age: 40 years; gender: male; disease state: Crohn's disease; tissue: colonic biopsy controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM646011 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Biopsy_ITB_012 Colonic biopsies, intestinal tuberculosis disease age: 26 years; gender: female; disease state: intestinal tuberculosis disease; tissue: colonic biopsy controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM646012 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Biopsy_ITB_026 Colonic biopsies, intestinal tuberculosis disease age: 40 years; gender: female; disease state: intestinal tuberculosis disease; tissue: colonic biopsy controlled vocabulary controlled vocabulary primary tissue match: biopsy

tissue colon GSE26305 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence colonic dataset_accession: GSE26305 dataset_title: Genome-wide gene expression analysis for target genes to differentiate patients with intestinal tuberculosis and Crohn’s disease organ... controlled vocabulary controlled vocabulary tissue match: colonic

tissue intestine GSE26305 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal dataset_accession: GSE26305 dataset_title: Genome-wide gene expression analysis for target genes to differentiate patients with intestinal tuberculosis and Crohn’s disease organ... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue colon GSM645979 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence colonic Biopsy_Control_015 Colonic biopsies, control age: 23 years; gender: male; sample type: control; tissue: colonic biopsy controlled vocabulary controlled vocabulary tissue match: colonic

tissue colon GSM646008 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence colonic Biopsy_Control_030 Colonic biopsies, control age: 65 years; gender: female; sample type: control; tissue: colonic biopsy controlled vocabulary controlled vocabulary tissue match: colonic

tissue colon GSM646009 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence colonic Biopsy_CD_017 Colonic biopsies, Crohn's disease age: 29 years; gender: male; disease state: Crohn's disease; tissue: colonic biopsy controlled vocabulary controlled vocabulary tissue match: colonic

tissue colon GSM646010 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence colonic Biopsy_CD_024 Colonic biopsies, Crohn's disease age: 40 years; gender: male; disease state: Crohn's disease; tissue: colonic biopsy controlled vocabulary controlled vocabulary tissue match: colonic

tissue colon GSM646011 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence colonic Biopsy_ITB_012 Colonic biopsies, intestinal tuberculosis disease age: 26 years; gender: female; disease state: intestinal tuberculosis disease; tissue: colonic biopsy controlled vocabulary controlled vocabulary tissue match: colonic

tissue intestine GSM646011 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal Biopsy_ITB_012 Colonic biopsies, intestinal tuberculosis disease age: 26 years; gender: female; disease state: intestinal tuberculosis disease; tissue: colonic biopsy controlled vocabulary controlled vocabulary tissue match: intestinal

tissue colon GSM646012 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence colonic Biopsy_ITB_026 Colonic biopsies, intestinal tuberculosis disease age: 40 years; gender: female; disease state: intestinal tuberculosis disease; tissue: colonic biopsy controlled vocabulary controlled vocabulary tissue match: colonic

tissue intestine GSM646012 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal Biopsy_ITB_026 Colonic biopsies, intestinal tuberculosis disease age: 40 years; gender: female; disease state: intestinal tuberculosis disease; tissue: colonic biopsy controlled vocabulary controlled vocabulary tissue match: intestinal

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	GSM646009	Biopsy_CD_017	Colonic biopsies, Crohn's disease Age: 29 years; Gender: Male; Disease state: Crohn's disease; Tissue: Colonic biopsy	Case marker detected.
Crohn's disease	Case	GSM646010	Biopsy_CD_024	Colonic biopsies, Crohn's disease Age: 40 years; Gender: Male; Disease state: Crohn's disease; Tissue: Colonic biopsy	Case marker detected.
Tuberculosis	Case	GSM646011	Biopsy_ITB_012	Colonic biopsies, intestinal tuberculosis disease Age: 26 years; Gender: Female; Disease state: Intestinal tuberculosis disease; Tissue: Colonic biopsy	Case marker detected.
Tuberculosis	Case	GSM646012	Biopsy_ITB_026	Colonic biopsies, intestinal tuberculosis disease Age: 40 years; Gender: Female; Disease state: Intestinal tuberculosis disease; Tissue: Colonic biopsy	Case marker detected.
Control	Control	GSM645979	Biopsy_Control_015	Colonic biopsies, control Age: 23 years; Gender: Male; Sample type: Control; Tissue: Colonic biopsy	Sample-local control marker detected.
Control	Control	GSM646008	Biopsy_Control_030	Colonic biopsies, control Age: 65 years; Gender: Female; Sample type: Control; Tissue: Colonic biopsy	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