Expression profiling in inflammatory bowel 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

10 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: 31 samples
Specimen: Biopsy
Reported/interpreted study design: Disease/model vs control Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Costello CM, Mah N, Häsler R, Lu T, Nikolaus S, Eickhoff H, Lehrach H, Schreiber S, Haesler R
Contact name: Robert Haesler
Submission date: 2004-08-27
Last update: 2012-03-15
Organization: University Clinic of Schleswig Holstein
Department: IKMB / 1st Dept. of Medicine
Public date: 2005-08-11
Experiment types: Expression profiling by array
Platforms: GPL284 Human UniGene Set RZPD 1
Series type: Series
SubSeries: Not available
BioProject: PRJNA90369

Summary

The series was designed to identify new genes involved in the pathophysiology of inflammatory bowel disease (Crohn's disease and ulcerative colitis). This series represents a group of 31 samples, subdivided into 3 groups: 1) Normal controls: 11 samples; 2) patients with Crohn's diseases: 10 samples; 3) patients with ulcerative colitis: 10 samples. Each sample originated from a different patient or normal control, in total n=31 individuals were examined. Keywords = Inflammatory bowel disease Keywords = Crohn's disease Keywords = ulcerative colitis Keywords = expression screening Keywords = expression profiling Keywords: other

Overall design

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 31 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 Dissection of the inflammatory bowel disease transcriptome using genome-wide cDNA microarrays. PLoS medicine, 2005 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

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

3/15 pts

Unassigned or review-needed samples remain before analysis.

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

10 samples are still unassigned.

Next Steps

Resolve unassigned or review-needed samples in the grouping table.

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

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

Needs review

0 review-needed samples and 10 unassigned samples remain.

Resolve ambiguous and unassigned samples before finalizing the contrast.

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.

One or more samples are unassigned and need manual grouping decisions.

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 10 samples
Likely control group Control 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: Biopsy. Comparison suitability: 0%.
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 16107186.
Publication context: Dissection of the inflammatory bowel disease transcriptome using genome-wide cDNA microarrays.. PLoS medicine, 2005. PMID 16107186. DOI 10.1371/journal.pmed.0020199.

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.
Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.

Normalized Fields

139 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source colon GSM29595 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM29596 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM29597 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM29598 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM29599 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM29600 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM29601 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM29602 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM29603 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM29604 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM29605 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM29606 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM29607 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM29608 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM29609 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM29610 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM29611 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM29612 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM29613 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM29614 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM29615 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM29616 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM29617 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM29618 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM29619 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM29620 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM29621 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM29622 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM29623 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM29624 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM29625 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon source_name: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

assay_type microarray GSE1710 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence microarray dataset_accession: GSE1710 dataset_title: Expression profiling in inflammatory bowel disease organism: Homo sapiens assay_type: microarray processed_data_available: true raw_dat... keyword match keyword match: microarray

collection_method biopsy GSM29595 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Control 01, NC01 sigmoid colon biopsy none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM29596 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Control 02, NC02 sigmoid colon biopsy none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM29597 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Control 03, NC03 sigmoid colon biopsy none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM29598 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Control 04, NC04 sigmoid colon biopsy none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM29599 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Control 05, NC05 sigmoid colon biopsy none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM29600 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Control 06, NC06 sigmoid colon biopsy none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM29601 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Control 07, NC07 sigmoid colon biopsy none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM29602 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Control 08, NC08 sigmoid colon biopsy none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM29603 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Control 09, NC09 sigmoid colon biopsy none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM29604 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Control 10, NC10 sigmoid colon biopsy none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM29605 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Control 11, NC11 sigmoid colon biopsy none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM29606 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Crohn 01, CD01 sigmoid colon biopsy none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM29607 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Crohn 02, CD02 sigmoid colon biopsy none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM29608 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Crohn 03, CD03 sigmoid colon biopsy none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM29609 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Crohn 04, CD04 sigmoid colon biopsy none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM29610 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Crohn 05, CD05 sigmoid colon biopsy none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM29611 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Crohn 06, CD06 sigmoid colon biopsy none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM29612 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Crohn 07, CD07 sigmoid colon biopsy none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM29613 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Crohn 08, CD08 sigmoid colon biopsy none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM29614 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Crohn 09, CD09 sigmoid colon biopsy none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM29615 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Crohn 10, CD10 sigmoid colon biopsy none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM29616 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Colitis 01, UC01 sigmoid colon biopsy none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM29617 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Colitis 02, UC02 sigmoid colon biopsy none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM29618 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Colitis 03, UC03 sigmoid colon biopsy none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM29619 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Colitis 04, UC04 sigmoid colon biopsy none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM29620 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Colitis 05, UC05 sigmoid colon biopsy none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM29621 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Colitis 06, UC06 sigmoid colon biopsy none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM29622 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Colitis 07, UC07 sigmoid colon biopsy none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM29623 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Colitis 08, UC08 sigmoid colon biopsy none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM29624 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Colitis 09, UC09 sigmoid colon biopsy none controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM29625 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Colitis 10, UC10 sigmoid colon biopsy none controlled vocabulary controlled vocabulary collection method match: biopsy

disease Crohn's disease GSE1710 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease dataset_accession: GSE1710 dataset_title: Expression profiling in inflammatory bowel disease organism: Homo sapiens assay_type: microarray processed_data_available: true raw_dat... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease inflammatory bowel disease GSE1710 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflammatory bowel disease dataset_accession: GSE1710 dataset_title: Expression profiling in inflammatory bowel disease organism: Homo sapiens assay_type: microarray processed_data_available: true raw_dat... controlled vocabulary controlled vocabulary disease match: inflammatory bowel disease

disease ulcerative colitis GSE1710 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis dataset_accession: GSE1710 dataset_title: Expression profiling in inflammatory bowel disease organism: Homo sapiens assay_type: microarray processed_data_available: true raw_dat... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease Crohn's disease GSM29606 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence Crohn Crohn 01, CD01 sigmoid colon biopsy none controlled vocabulary controlled vocabulary disease match: Crohn

disease Crohn's disease GSM29607 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence Crohn Crohn 02, CD02 sigmoid colon biopsy none controlled vocabulary controlled vocabulary disease match: Crohn

disease Crohn's disease GSM29608 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence Crohn Crohn 03, CD03 sigmoid colon biopsy none controlled vocabulary controlled vocabulary disease match: Crohn

disease Crohn's disease GSM29609 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence Crohn Crohn 04, CD04 sigmoid colon biopsy none controlled vocabulary controlled vocabulary disease match: Crohn

disease Crohn's disease GSM29610 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence Crohn Crohn 05, CD05 sigmoid colon biopsy none controlled vocabulary controlled vocabulary disease match: Crohn

disease Crohn's disease GSM29611 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence Crohn Crohn 06, CD06 sigmoid colon biopsy none controlled vocabulary controlled vocabulary disease match: Crohn

disease Crohn's disease GSM29612 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence Crohn Crohn 07, CD07 sigmoid colon biopsy none controlled vocabulary controlled vocabulary disease match: Crohn

disease Crohn's disease GSM29613 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence Crohn Crohn 08, CD08 sigmoid colon biopsy none controlled vocabulary controlled vocabulary disease match: Crohn

disease Crohn's disease GSM29614 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence Crohn Crohn 09, CD09 sigmoid colon biopsy none controlled vocabulary controlled vocabulary disease match: Crohn

disease Crohn's disease GSM29615 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence Crohn Crohn 10, CD10 sigmoid colon biopsy none controlled vocabulary controlled vocabulary disease match: Crohn

organism Homo sapiens GSE1710 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE1710 dataset_title: Expression profiling in inflammatory bowel disease organism: Homo sapiens assay_type: microarray processed_data_available: true raw_dat... keyword match keyword match: homo sapiens

primary_tissue primary tissue GSM29595 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Control 01, NC01 sigmoid colon biopsy none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM29596 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Control 02, NC02 sigmoid colon biopsy none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM29597 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Control 03, NC03 sigmoid colon biopsy none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM29598 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Control 04, NC04 sigmoid colon biopsy none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM29599 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Control 05, NC05 sigmoid colon biopsy none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM29600 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Control 06, NC06 sigmoid colon biopsy none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM29601 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Control 07, NC07 sigmoid colon biopsy none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM29602 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Control 08, NC08 sigmoid colon biopsy none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM29603 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Control 09, NC09 sigmoid colon biopsy none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM29604 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Control 10, NC10 sigmoid colon biopsy none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM29605 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Control 11, NC11 sigmoid colon biopsy none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM29606 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Crohn 01, CD01 sigmoid colon biopsy none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM29607 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Crohn 02, CD02 sigmoid colon biopsy none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM29608 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Crohn 03, CD03 sigmoid colon biopsy none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM29609 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Crohn 04, CD04 sigmoid colon biopsy none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM29610 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Crohn 05, CD05 sigmoid colon biopsy none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM29611 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Crohn 06, CD06 sigmoid colon biopsy none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM29612 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Crohn 07, CD07 sigmoid colon biopsy none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM29613 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Crohn 08, CD08 sigmoid colon biopsy none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM29614 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Crohn 09, CD09 sigmoid colon biopsy none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM29615 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Crohn 10, CD10 sigmoid colon biopsy none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM29616 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Colitis 01, UC01 sigmoid colon biopsy none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM29617 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Colitis 02, UC02 sigmoid colon biopsy none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM29618 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Colitis 03, UC03 sigmoid colon biopsy none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM29619 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Colitis 04, UC04 sigmoid colon biopsy none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM29620 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Colitis 05, UC05 sigmoid colon biopsy none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM29621 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Colitis 06, UC06 sigmoid colon biopsy none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM29622 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Colitis 07, UC07 sigmoid colon biopsy none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM29623 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Colitis 08, UC08 sigmoid colon biopsy none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM29624 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Colitis 09, UC09 sigmoid colon biopsy none controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM29625 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Colitis 10, UC10 sigmoid colon biopsy none controlled vocabulary controlled vocabulary primary tissue match: biopsy

tissue colon GSM29595 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Control 01, NC01 sigmoid colon biopsy none controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM29596 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Control 02, NC02 sigmoid colon biopsy none controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM29597 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Control 03, NC03 sigmoid colon biopsy none controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM29598 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Control 04, NC04 sigmoid colon biopsy none controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM29599 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Control 05, NC05 sigmoid colon biopsy none controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM29600 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Control 06, NC06 sigmoid colon biopsy none controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM29601 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Control 07, NC07 sigmoid colon biopsy none controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM29602 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Control 08, NC08 sigmoid colon biopsy none controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM29603 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Control 09, NC09 sigmoid colon biopsy none controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM29604 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Control 10, NC10 sigmoid colon biopsy none controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM29605 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Control 11, NC11 sigmoid colon biopsy none controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM29606 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Crohn 01, CD01 sigmoid colon biopsy none controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM29607 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Crohn 02, CD02 sigmoid colon biopsy none controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM29608 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Crohn 03, CD03 sigmoid colon biopsy none controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM29609 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Crohn 04, CD04 sigmoid colon biopsy none controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM29610 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Crohn 05, CD05 sigmoid colon biopsy none controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM29611 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Crohn 06, CD06 sigmoid colon biopsy none controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM29612 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Crohn 07, CD07 sigmoid colon biopsy none controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM29613 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Crohn 08, CD08 sigmoid colon biopsy none controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM29614 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Crohn 09, CD09 sigmoid colon biopsy none controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM29615 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Crohn 10, CD10 sigmoid colon biopsy none controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM29616 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Colitis 01, UC01 sigmoid colon biopsy none controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM29617 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Colitis 02, UC02 sigmoid colon biopsy none controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM29618 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Colitis 03, UC03 sigmoid colon biopsy none controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM29619 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Colitis 04, UC04 sigmoid colon biopsy none controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM29620 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Colitis 05, UC05 sigmoid colon biopsy none controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM29621 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Colitis 06, UC06 sigmoid colon biopsy none controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM29622 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Colitis 07, UC07 sigmoid colon biopsy none controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM29623 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Colitis 08, UC08 sigmoid colon biopsy none controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM29624 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Colitis 09, UC09 sigmoid colon biopsy none controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM29625 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Colitis 10, UC10 sigmoid colon biopsy none controlled vocabulary controlled vocabulary tissue match: colon

Sample Group Preview

31 rows shown Show Hide

Study totals: Case 10 | Control 11 | Unassigned 10 | Excluded 0 | Ambiguous 0 31 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Crohn's disease	Case	GSM29606	Crohn 01, CD01	Sigmoid colon biopsy None	Case marker detected.
Crohn's disease	Case	GSM29607	Crohn 02, CD02	Sigmoid colon biopsy None	Case marker detected.
Crohn's disease	Case	GSM29608	Crohn 03, CD03	Sigmoid colon biopsy None	Case marker detected.
Crohn's disease	Case	GSM29609	Crohn 04, CD04	Sigmoid colon biopsy None	Case marker detected.
Crohn's disease	Case	GSM29610	Crohn 05, CD05	Sigmoid colon biopsy None	Case marker detected.
Crohn's disease	Case	GSM29611	Crohn 06, CD06	Sigmoid colon biopsy None	Case marker detected.
Crohn's disease	Case	GSM29612	Crohn 07, CD07	Sigmoid colon biopsy None	Case marker detected.
Crohn's disease	Case	GSM29613	Crohn 08, CD08	Sigmoid colon biopsy None	Case marker detected.
Crohn's disease	Case	GSM29614	Crohn 09, CD09	Sigmoid colon biopsy None	Case marker detected.
Crohn's disease	Case	GSM29615	Crohn 10, CD10	Sigmoid colon biopsy None	Case marker detected.
Control	Control	GSM29595	Control 01, NC01	Sigmoid colon biopsy None	Sample-local control marker detected.
Control	Control	GSM29596	Control 02, NC02	Sigmoid colon biopsy None	Sample-local control marker detected.
Control	Control	GSM29597	Control 03, NC03	Sigmoid colon biopsy None	Sample-local control marker detected.
Control	Control	GSM29598	Control 04, NC04	Sigmoid colon biopsy None	Sample-local control marker detected.
Control	Control	GSM29599	Control 05, NC05	Sigmoid colon biopsy None	Sample-local control marker detected.
Control	Control	GSM29600	Control 06, NC06	Sigmoid colon biopsy None	Sample-local control marker detected.
Control	Control	GSM29601	Control 07, NC07	Sigmoid colon biopsy None	Sample-local control marker detected.
Control	Control	GSM29602	Control 08, NC08	Sigmoid colon biopsy None	Sample-local control marker detected.
Control	Control	GSM29603	Control 09, NC09	Sigmoid colon biopsy None	Sample-local control marker detected.
Control	Control	GSM29604	Control 10, NC10	Sigmoid colon biopsy None	Sample-local control marker detected.
Control	Control	GSM29605	Control 11, NC11	Sigmoid colon biopsy None	Sample-local control marker detected.
Unassigned	Unassigned	GSM29616	Colitis 01, UC01	Sigmoid colon biopsy None	No explicit case or control marker detected.
Unassigned	Unassigned	GSM29617	Colitis 02, UC02	Sigmoid colon biopsy None	No explicit case or control marker detected.
Unassigned	Unassigned	GSM29618	Colitis 03, UC03	Sigmoid colon biopsy None	No explicit case or control marker detected.
Unassigned	Unassigned	GSM29619	Colitis 04, UC04	Sigmoid colon biopsy None	No explicit case or control marker detected.
Unassigned	Unassigned	GSM29620	Colitis 05, UC05	Sigmoid colon biopsy None	No explicit case or control marker detected.
Unassigned	Unassigned	GSM29621	Colitis 06, UC06	Sigmoid colon biopsy None	No explicit case or control marker detected.
Unassigned	Unassigned	GSM29622	Colitis 07, UC07	Sigmoid colon biopsy None	No explicit case or control marker detected.
Unassigned	Unassigned	GSM29623	Colitis 08, UC08	Sigmoid colon biopsy None	No explicit case or control marker detected.
Unassigned	Unassigned	GSM29624	Colitis 09, UC09	Sigmoid colon biopsy None	No explicit case or control marker detected.
Unassigned	Unassigned	GSM29625	Colitis 10, UC10	Sigmoid colon biopsy None	No explicit case or 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

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Next Steps

Analysis Preparation Checklist

Bioinformatician Review

Why This Is Ranked Here

Applied Review Decisions

Derived Classifications

Intent Interpretation

Ranking Facts

Supporting evidence

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Sample Group Preview

Use as Discovery Cohort