GSE69762

Gene expression of human small intestine generated by biopsy specimens

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

16 case / 0 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: 30 samples
Specimen: Biopsy
Reported/interpreted study design: Unclear study design Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Tsuchiya K, Hayashi R, Horita N
Contact name: Kiichiro Tsuchiya
Submission date: 2015-06-10
Last update: 2018-07-26
Organization: Tokyo Medical and Dental University
Department: Not available
Public date: 2015-06-11
Experiment types: Expression profiling by array
Platforms: GPL6244 [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]
Series type: Series
SubSeries: Not available
BioProject: PRJNA286681

Summary

The entire small intestine was obseved by balloon endoscopy. Biopsy specimens were taken from jejunum, ileum and colon, respectively.

Overall design

Four crohn disease patients and four nonIBD controls were compared.

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 30 GSM samples	Primary source
recount3	Planned trusted source for processed count availability.	No match found
Expression Atlas	Curated expression experiment linkage and source URL. Expression Atlas accession E-GEOD-69762	Available
PubMed	Primary GEO citations and related PubMed articles that mention this dataset. 2 linked publications 2 DOIs Primary publication Reduced Human α-defensin 6 in Noninflamed Jejunal Tissue of Patients with Crohn's Disease. Inflammatory bowel diseases, 2016 PubMed DOI Related publications Identifying the importance of PCK1 in maintaining ileal epithelial barrier integrity in Crohn's disease. Gene, 2024 PubMed DOI	Available

Metadata Quality Components

Persisted metadata quality

93 pts

Clarity: 93%
Weight: 100 pts

Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Only one side of the comparison is clearly grouped. 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

Not ready

43% DE readiness

Contrast completeness

10/25 pts

Only one side of the contrast is present; downstream DE needs both groups.

Minimum group size

0/20 pts

Minimum group size cannot be evaluated until a complete contrast exists.

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

0/10 pts

Critical warnings must be resolved before downstream analysis.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

No complete case/control contrast is available.
14 samples are still unassigned.
Critical dataset warnings must be resolved.

Next Steps

Resolve unassigned or review-needed samples in the grouping table.
Resolve critical warnings before downstream analysis.

Analysis Preparation Checklist

3/6 ready

Group labels reviewed

Blocked

No complete case/control grouping exists yet.

Review the sample grouping table and assign both case and control groups.

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

Needs review

0 review-needed samples and 14 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.

Analysis preparation checklist contains blocked items.

No complete case/control or treatment/control contrast is available.

At least one comparison group has fewer than two samples.

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

Critical dataset warnings are present.

Assay context may require expert handling before DESeq2-style analysis.

Study design is model-system or unclear and should be reviewed before 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 Disease context came from Normalization rules.
Likely case group Crohn's disease 16 samples
Likely control group No control group detected 0 samples

Intent Interpretation

Downgrade or exclusion reason Comparison: Unclear study design. Specimen: Biopsy. Comparison suitability: 0%. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

Interpreted disease metadata: Crohn's disease, Inflammatory bowel disease.
Processed data is available for downstream review.
External evidence: Expression Atlas curated experiment link is available.
External evidence: PubMed links 2 publications; 2 DOIs available: PMID 26891258, PMID 39159791.
Publication context: Reduced Human α-defensin 6 in Noninflamed Jejunal Tissue of Patients with Crohn's Disease.. Inflammatory bowel diseases, 2016. PMID 26891258. DOI 10.1097/MIB.0000000000000707.
Publication context: Identifying the importance of PCK1 in maintaining ileal epithelial barrier integrity in Crohn's disease.. Gene, 2024. PMID 39159791. DOI 10.1016/j.gene.2024.148872.

Cautions

Comparison: Unclear study design. Specimen: Biopsy. Comparison suitability: 0%.
Downgraded for tissue search because study design or specimen source is unclear.
Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
Overall score capped because comparison suitability is weak for the selected search intent.
Missing or unclear metadata. Comparison - Unclear study design. Specimen - Biopsy. Comparison suitability: 0%.
Missing or unclear metadata. Downgraded for tissue search because study design or specimen source is unclear.
Publication context: Reduced Human α-defensin 6 in Noninflamed Jejunal Tissue of Patients with Crohn's Disease.. Inflammatory bowel diseases, 2016. PMID 26891258. DOI 10.1097/MIB.0000000000000707.
Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

No clear control group was detected from normalized metadata.
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.
Patient-tissue tumor-normal intent requires clear tumor-normal grouping.

Normalized Fields

108 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source ileum GSM1708493 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ileum tissue: nonIBD ileum lower sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1708494 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: nonIBD ascending colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source ileum GSM1708497 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ileum tissue: IBD ileum upper sample-anatomical-source-v1 sample-local anatomical source

anatomical_source ileum GSM1708498 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ileum tissue: IBD ileum middle sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1708499 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: IBD ascending colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source ileum GSM1708511 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ileum tissue: nonIBD Ileum Upper sample-anatomical-source-v1 sample-local anatomical source

anatomical_source ileum GSM1708512 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ileum tissue: nonIBD Ileum Middle sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1708513 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: nonIBD colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source ileum GSM1708518 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ileum tissue: CD Ileum Upper sample-anatomical-source-v1 sample-local anatomical source

anatomical_source ileum GSM1708519 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ileum tissue: CD Ileum Lower sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1708520 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: CD colon sample-anatomical-source-v1 sample-local anatomical source

assay_type microarray GSE69762 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence microarray dataset_accession: GSE69762 dataset_title: Gene expression of human small intestine generated by biopsy specimens organism: Homo sapiens assay_type: microarray processed_data_av... keyword match keyword match: microarray

collection_method biopsy GSM1708491 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy nonIBD_jejunum_upper biopsy specimen disease state: nonIBD; tissue: nonIBD jejunum upper controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1708492 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy nonIBD_jejunum_lower biopsy specimen disease state: nonIBD; tissue: nonIBD jejunum lower controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1708493 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy nonIBD_ileum_lower biopsy specimen disease state: nonIBD; tissue: nonIBD ileum lower controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1708494 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy nonIBD_ascending colon biopsy specimen disease state: nonIBD; tissue: nonIBD ascending colon controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1708495 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy IBD_jejunum_upper biopsy specimen disease state: Crohn Disease; tissue: IBD jejunum upper controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1708496 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy IBD_jejunum_lower biopsy specimen disease state: Crohn Disease; tissue: IBD jejunum lower controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1708497 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy IBD_ileum_upper biopsy specimen disease state: Crohn Disease; tissue: IBD ileum upper controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1708498 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy IBD_ileum_middle biopsy specimen disease state: Crohn Disease; tissue: IBD ileum middle controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1708499 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy IBD_ascending colon biopsy specimen disease state: Crohn Disease; tissue: IBD ascending colon controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1708500 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.6_nonIBD_Jejunum_Upper biopsy specimen disease state: nonIBD; tissue: nonIBD Jejunum Upper controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1708501 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.6_nonIBD_Jejunum_Lower biopsy specimen disease state: nonIBD; tissue: nonIBD Jejunum Lower controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1708502 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No7_nonIBD_Jejunum_Upper biopsy specimen disease state: nonIBD; tissue: nonIBD Jejunum Upper controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1708503 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No7_nonIBD_Jejunum_Lower biopsy specimen disease state: nonIBD; tissue: nonIBD Jejunum Lower controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1708504 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.9_CD_Jejunum_Upper biopsy specimen disease state: Crohn Disease; tissue: CD Jejunum Upper controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1708505 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.9_CD_Jejunum_Lower biopsy specimen disease state: Crohn Disease; tissue: CD Jejunum Lower controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1708506 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.11_CD_Jejunum_Upper biopsy specimen disease state: Crohn Disease; tissue: CD Jejunum Upper controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1708507 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.11_CD_Jejunum_Lower biopsy specimen disease state: Crohn Disease; tissue: CD Jejunum Lower controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1708508 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.9_nonIBD_Jejunum_Upper biopsy specimen disease state: nonIBD; tissue: nonIBD Jejunum Upper controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1708509 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.9_nonIBD_Jejunum_Middle biopsy specimen disease state: nonIBD; tissue: nonIBD Jejunum Middle controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1708510 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.9_nonIBD_Jejunum_Lower biopsy specimen disease state: nonIBD; tissue: nonIBD Jejunum Lower controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1708511 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.9_nonIBD_Ileum_Upper biopsy specimen disease state: nonIBD; tissue: nonIBD Ileum Upper controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1708512 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.9_nonIBD_Ileum_Middle biopsy specimen disease state: nonIBD; tissue: nonIBD Ileum Middle controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1708513 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.9_nonIBD_colon biopsy specimen disease state: nonIBD; tissue: nonIBD colon controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1708514 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.12_CD_Jejunum_Upper_np biopsy specimen disease state: Crohn Disease; tissue: CD Jejunum Upper np controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1708515 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.12_CD_Jejunum_Upper_ulcer biopsy specimen disease state: Crohn Disease; tissue: CD Jejunum Upper ulcer controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1708516 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.12_CD_Jejunum_Middle biopsy specimen disease state: Crohn Disease; tissue: CD Jejunum Middle controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1708517 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.12_CD_Jejunum_ Lower biopsy specimen disease state: Crohn Disease; tissue: CD Jejunum Lower controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1708518 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.12_CD_Ileum_Upper biopsy specimen disease state: Crohn Disease; tissue: CD Ileum Upper controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1708519 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.12_CD_Ileum_ Lower biopsy specimen disease state: Crohn Disease; tissue: CD Ileum Lower controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1708520 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.12_CD_colon biopsy specimen disease state: Crohn Disease; tissue: CD colon controlled vocabulary controlled vocabulary collection method match: biopsy

disease Crohn's disease GSE69762 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn disease dataset_accession: GSE69762 dataset_title: Gene expression of human small intestine generated by biopsy specimens organism: Homo sapiens assay_type: microarray processed_data_av... controlled vocabulary controlled vocabulary disease match: Crohn disease

disease Crohn's disease GSM1708495 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn disease IBD_jejunum_upper biopsy specimen disease state: Crohn Disease; tissue: IBD jejunum upper controlled vocabulary controlled vocabulary disease match: Crohn disease

disease inflammatory bowel disease GSM1708495 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ibd IBD_jejunum_upper biopsy specimen disease state: Crohn Disease; tissue: IBD jejunum upper controlled vocabulary controlled vocabulary disease match: ibd

disease Crohn's disease GSM1708496 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn disease IBD_jejunum_lower biopsy specimen disease state: Crohn Disease; tissue: IBD jejunum lower controlled vocabulary controlled vocabulary disease match: Crohn disease

disease inflammatory bowel disease GSM1708496 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ibd IBD_jejunum_lower biopsy specimen disease state: Crohn Disease; tissue: IBD jejunum lower controlled vocabulary controlled vocabulary disease match: ibd

disease Crohn's disease GSM1708497 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn disease IBD_ileum_upper biopsy specimen disease state: Crohn Disease; tissue: IBD ileum upper controlled vocabulary controlled vocabulary disease match: Crohn disease

disease inflammatory bowel disease GSM1708497 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ibd IBD_ileum_upper biopsy specimen disease state: Crohn Disease; tissue: IBD ileum upper controlled vocabulary controlled vocabulary disease match: ibd

disease Crohn's disease GSM1708498 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn disease IBD_ileum_middle biopsy specimen disease state: Crohn Disease; tissue: IBD ileum middle controlled vocabulary controlled vocabulary disease match: Crohn disease

disease inflammatory bowel disease GSM1708498 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ibd IBD_ileum_middle biopsy specimen disease state: Crohn Disease; tissue: IBD ileum middle controlled vocabulary controlled vocabulary disease match: ibd

disease Crohn's disease GSM1708499 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn disease IBD_ascending colon biopsy specimen disease state: Crohn Disease; tissue: IBD ascending colon controlled vocabulary controlled vocabulary disease match: Crohn disease

disease inflammatory bowel disease GSM1708499 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ibd IBD_ascending colon biopsy specimen disease state: Crohn Disease; tissue: IBD ascending colon controlled vocabulary controlled vocabulary disease match: ibd

disease Crohn's disease GSM1708504 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn disease No.9_CD_Jejunum_Upper biopsy specimen disease state: Crohn Disease; tissue: CD Jejunum Upper controlled vocabulary controlled vocabulary disease match: Crohn disease

disease Crohn's disease GSM1708505 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn disease No.9_CD_Jejunum_Lower biopsy specimen disease state: Crohn Disease; tissue: CD Jejunum Lower controlled vocabulary controlled vocabulary disease match: Crohn disease

disease Crohn's disease GSM1708506 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn disease No.11_CD_Jejunum_Upper biopsy specimen disease state: Crohn Disease; tissue: CD Jejunum Upper controlled vocabulary controlled vocabulary disease match: Crohn disease

disease Crohn's disease GSM1708507 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn disease No.11_CD_Jejunum_Lower biopsy specimen disease state: Crohn Disease; tissue: CD Jejunum Lower controlled vocabulary controlled vocabulary disease match: Crohn disease

disease Crohn's disease GSM1708514 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn disease No.12_CD_Jejunum_Upper_np biopsy specimen disease state: Crohn Disease; tissue: CD Jejunum Upper np controlled vocabulary controlled vocabulary disease match: Crohn disease

disease Crohn's disease GSM1708515 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn disease No.12_CD_Jejunum_Upper_ulcer biopsy specimen disease state: Crohn Disease; tissue: CD Jejunum Upper ulcer controlled vocabulary controlled vocabulary disease match: Crohn disease

disease Crohn's disease GSM1708516 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn disease No.12_CD_Jejunum_Middle biopsy specimen disease state: Crohn Disease; tissue: CD Jejunum Middle controlled vocabulary controlled vocabulary disease match: Crohn disease

disease Crohn's disease GSM1708517 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn disease No.12_CD_Jejunum_ Lower biopsy specimen disease state: Crohn Disease; tissue: CD Jejunum Lower controlled vocabulary controlled vocabulary disease match: Crohn disease

disease Crohn's disease GSM1708518 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn disease No.12_CD_Ileum_Upper biopsy specimen disease state: Crohn Disease; tissue: CD Ileum Upper controlled vocabulary controlled vocabulary disease match: Crohn disease

disease Crohn's disease GSM1708519 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn disease No.12_CD_Ileum_ Lower biopsy specimen disease state: Crohn Disease; tissue: CD Ileum Lower controlled vocabulary controlled vocabulary disease match: Crohn disease

disease Crohn's disease GSM1708520 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn disease No.12_CD_colon biopsy specimen disease state: Crohn Disease; tissue: CD colon controlled vocabulary controlled vocabulary disease match: Crohn disease

organism Homo sapiens GSE69762 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE69762 dataset_title: Gene expression of human small intestine generated by biopsy specimens organism: Homo sapiens assay_type: microarray processed_data_av... keyword match keyword match: homo sapiens

primary_tissue primary tissue GSM1708491 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy nonIBD_jejunum_upper biopsy specimen disease state: nonIBD; tissue: nonIBD jejunum upper controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1708492 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy nonIBD_jejunum_lower biopsy specimen disease state: nonIBD; tissue: nonIBD jejunum lower controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1708493 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy nonIBD_ileum_lower biopsy specimen disease state: nonIBD; tissue: nonIBD ileum lower controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1708494 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy nonIBD_ascending colon biopsy specimen disease state: nonIBD; tissue: nonIBD ascending colon controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1708495 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy IBD_jejunum_upper biopsy specimen disease state: Crohn Disease; tissue: IBD jejunum upper controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1708496 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy IBD_jejunum_lower biopsy specimen disease state: Crohn Disease; tissue: IBD jejunum lower controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1708497 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy IBD_ileum_upper biopsy specimen disease state: Crohn Disease; tissue: IBD ileum upper controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1708498 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy IBD_ileum_middle biopsy specimen disease state: Crohn Disease; tissue: IBD ileum middle controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1708499 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy IBD_ascending colon biopsy specimen disease state: Crohn Disease; tissue: IBD ascending colon controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1708500 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.6_nonIBD_Jejunum_Upper biopsy specimen disease state: nonIBD; tissue: nonIBD Jejunum Upper controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1708501 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.6_nonIBD_Jejunum_Lower biopsy specimen disease state: nonIBD; tissue: nonIBD Jejunum Lower controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1708502 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No7_nonIBD_Jejunum_Upper biopsy specimen disease state: nonIBD; tissue: nonIBD Jejunum Upper controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1708503 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No7_nonIBD_Jejunum_Lower biopsy specimen disease state: nonIBD; tissue: nonIBD Jejunum Lower controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1708504 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.9_CD_Jejunum_Upper biopsy specimen disease state: Crohn Disease; tissue: CD Jejunum Upper controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1708505 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.9_CD_Jejunum_Lower biopsy specimen disease state: Crohn Disease; tissue: CD Jejunum Lower controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1708506 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.11_CD_Jejunum_Upper biopsy specimen disease state: Crohn Disease; tissue: CD Jejunum Upper controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1708507 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.11_CD_Jejunum_Lower biopsy specimen disease state: Crohn Disease; tissue: CD Jejunum Lower controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1708508 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.9_nonIBD_Jejunum_Upper biopsy specimen disease state: nonIBD; tissue: nonIBD Jejunum Upper controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1708509 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.9_nonIBD_Jejunum_Middle biopsy specimen disease state: nonIBD; tissue: nonIBD Jejunum Middle controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1708510 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.9_nonIBD_Jejunum_Lower biopsy specimen disease state: nonIBD; tissue: nonIBD Jejunum Lower controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1708511 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.9_nonIBD_Ileum_Upper biopsy specimen disease state: nonIBD; tissue: nonIBD Ileum Upper controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1708512 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.9_nonIBD_Ileum_Middle biopsy specimen disease state: nonIBD; tissue: nonIBD Ileum Middle controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1708513 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.9_nonIBD_colon biopsy specimen disease state: nonIBD; tissue: nonIBD colon controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1708514 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.12_CD_Jejunum_Upper_np biopsy specimen disease state: Crohn Disease; tissue: CD Jejunum Upper np controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1708515 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.12_CD_Jejunum_Upper_ulcer biopsy specimen disease state: Crohn Disease; tissue: CD Jejunum Upper ulcer controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1708516 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.12_CD_Jejunum_Middle biopsy specimen disease state: Crohn Disease; tissue: CD Jejunum Middle controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1708517 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.12_CD_Jejunum_ Lower biopsy specimen disease state: Crohn Disease; tissue: CD Jejunum Lower controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1708518 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.12_CD_Ileum_Upper biopsy specimen disease state: Crohn Disease; tissue: CD Ileum Upper controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1708519 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.12_CD_Ileum_ Lower biopsy specimen disease state: Crohn Disease; tissue: CD Ileum Lower controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1708520 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy No.12_CD_colon biopsy specimen disease state: Crohn Disease; tissue: CD colon controlled vocabulary controlled vocabulary primary tissue match: biopsy

tissue colon GSE69762 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon dataset_accession: GSE69762 dataset_title: Gene expression of human small intestine generated by biopsy specimens organism: Homo sapiens assay_type: microarray processed_data_av... controlled vocabulary controlled vocabulary tissue match: colon

tissue intestine GSE69762 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence intestine dataset_accession: GSE69762 dataset_title: Gene expression of human small intestine generated by biopsy specimens organism: Homo sapiens assay_type: microarray processed_data_av... controlled vocabulary controlled vocabulary tissue match: intestine

tissue intestine GSM1708493 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ileum nonIBD_ileum_lower biopsy specimen disease state: nonIBD; tissue: nonIBD ileum lower controlled vocabulary controlled vocabulary tissue match: ileum

tissue colon GSM1708494 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon nonIBD_ascending colon biopsy specimen disease state: nonIBD; tissue: nonIBD ascending colon controlled vocabulary controlled vocabulary tissue match: colon

tissue intestine GSM1708497 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ileum IBD_ileum_upper biopsy specimen disease state: Crohn Disease; tissue: IBD ileum upper controlled vocabulary controlled vocabulary tissue match: ileum

tissue intestine GSM1708498 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ileum IBD_ileum_middle biopsy specimen disease state: Crohn Disease; tissue: IBD ileum middle controlled vocabulary controlled vocabulary tissue match: ileum

tissue colon GSM1708499 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon IBD_ascending colon biopsy specimen disease state: Crohn Disease; tissue: IBD ascending colon controlled vocabulary controlled vocabulary tissue match: colon

tissue intestine GSM1708511 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ileum No.9_nonIBD_Ileum_Upper biopsy specimen disease state: nonIBD; tissue: nonIBD Ileum Upper controlled vocabulary controlled vocabulary tissue match: ileum

tissue intestine GSM1708512 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ileum No.9_nonIBD_Ileum_Middle biopsy specimen disease state: nonIBD; tissue: nonIBD Ileum Middle controlled vocabulary controlled vocabulary tissue match: ileum

tissue colon GSM1708513 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon No.9_nonIBD_colon biopsy specimen disease state: nonIBD; tissue: nonIBD colon controlled vocabulary controlled vocabulary tissue match: colon

tissue intestine GSM1708518 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ileum No.12_CD_Ileum_Upper biopsy specimen disease state: Crohn Disease; tissue: CD Ileum Upper controlled vocabulary controlled vocabulary tissue match: ileum

tissue intestine GSM1708519 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ileum No.12_CD_Ileum_ Lower biopsy specimen disease state: Crohn Disease; tissue: CD Ileum Lower controlled vocabulary controlled vocabulary tissue match: ileum

tissue colon GSM1708520 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon No.12_CD_colon biopsy specimen disease state: Crohn Disease; tissue: CD colon controlled vocabulary controlled vocabulary tissue match: colon

Sample Group Preview

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Study totals: Case 16 | Control 0 | Unassigned 14 | Excluded 0 | Ambiguous 0 30 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Crohn's disease	Case	GSM1708495	IBD_jejunum_upper	Biopsy specimen Disease state: Crohn Disease; Tissue: IBD jejunum upper	Case marker detected.
Crohn's disease	Case	GSM1708496	IBD_jejunum_lower	Biopsy specimen Disease state: Crohn Disease; Tissue: IBD jejunum lower	Case marker detected.
Crohn's disease	Case	GSM1708497	IBD_ileum_upper	Biopsy specimen Disease state: Crohn Disease; Tissue: IBD ileum upper	Case marker detected.
Crohn's disease	Case	GSM1708498	IBD_ileum_middle	Biopsy specimen Disease state: Crohn Disease; Tissue: IBD ileum middle	Case marker detected.
Crohn's disease	Case	GSM1708499	IBD_ascending colon	Biopsy specimen Disease state: Crohn Disease; Tissue: IBD ascending colon	Case marker detected.
Crohn's disease	Case	GSM1708504	No.9_CD_Jejunum_Upper	Biopsy specimen Disease state: Crohn Disease; Tissue: CD Jejunum Upper	Case marker detected.
Crohn's disease	Case	GSM1708505	No.9_CD_Jejunum_Lower	Biopsy specimen Disease state: Crohn Disease; Tissue: CD Jejunum Lower	Case marker detected.
Crohn's disease	Case	GSM1708506	No.11_CD_Jejunum_Upper	Biopsy specimen Disease state: Crohn Disease; Tissue: CD Jejunum Upper	Case marker detected.
Crohn's disease	Case	GSM1708507	No.11_CD_Jejunum_Lower	Biopsy specimen Disease state: Crohn Disease; Tissue: CD Jejunum Lower	Case marker detected.
Crohn's disease	Case	GSM1708514	No.12_CD_Jejunum_Upper_np	Biopsy specimen Disease state: Crohn Disease; Tissue: CD Jejunum Upper np	Case marker detected.
Crohn's disease	Case	GSM1708515	No.12_CD_Jejunum_Upper_ulcer	Biopsy specimen Disease state: Crohn Disease; Tissue: CD Jejunum Upper ulcer	Case marker detected.
Crohn's disease	Case	GSM1708516	No.12_CD_Jejunum_Middle	Biopsy specimen Disease state: Crohn Disease; Tissue: CD Jejunum Middle	Case marker detected.
Crohn's disease	Case	GSM1708517	No.12_CD_Jejunum_ Lower	Biopsy specimen Disease state: Crohn Disease; Tissue: CD Jejunum Lower	Case marker detected.
Crohn's disease	Case	GSM1708518	No.12_CD_Ileum_Upper	Biopsy specimen Disease state: Crohn Disease; Tissue: CD Ileum Upper	Case marker detected.
Crohn's disease	Case	GSM1708519	No.12_CD_Ileum_ Lower	Biopsy specimen Disease state: Crohn Disease; Tissue: CD Ileum Lower	Case marker detected.
Crohn's disease	Case	GSM1708520	No.12_CD_colon	Biopsy specimen Disease state: Crohn Disease; Tissue: CD colon	Case marker detected.
Unassigned	Unassigned	GSM1708491	NonIBD_jejunum_upper	Biopsy specimen Disease state: NonIBD; Tissue: NonIBD jejunum upper	No explicit case or control marker detected.
Unassigned	Unassigned	GSM1708492	NonIBD_jejunum_lower	Biopsy specimen Disease state: NonIBD; Tissue: NonIBD jejunum lower	No explicit case or control marker detected.
Unassigned	Unassigned	GSM1708493	NonIBD_ileum_lower	Biopsy specimen Disease state: NonIBD; Tissue: NonIBD ileum lower	No explicit case or control marker detected.
Unassigned	Unassigned	GSM1708494	NonIBD_ascending colon	Biopsy specimen Disease state: NonIBD; Tissue: NonIBD ascending colon	No explicit case or control marker detected.
Unassigned	Unassigned	GSM1708500	No.6_nonIBD_Jejunum_Upper	Biopsy specimen Disease state: NonIBD; Tissue: NonIBD Jejunum Upper	No explicit case or control marker detected.
Unassigned	Unassigned	GSM1708501	No.6_nonIBD_Jejunum_Lower	Biopsy specimen Disease state: NonIBD; Tissue: NonIBD Jejunum Lower	No explicit case or control marker detected.
Unassigned	Unassigned	GSM1708502	No7_nonIBD_Jejunum_Upper	Biopsy specimen Disease state: NonIBD; Tissue: NonIBD Jejunum Upper	No explicit case or control marker detected.
Unassigned	Unassigned	GSM1708503	No7_nonIBD_Jejunum_Lower	Biopsy specimen Disease state: NonIBD; Tissue: NonIBD Jejunum Lower	No explicit case or control marker detected.
Unassigned	Unassigned	GSM1708508	No.9_nonIBD_Jejunum_Upper	Biopsy specimen Disease state: NonIBD; Tissue: NonIBD Jejunum Upper	No explicit case or control marker detected.
Unassigned	Unassigned	GSM1708509	No.9_nonIBD_Jejunum_Middle	Biopsy specimen Disease state: NonIBD; Tissue: NonIBD Jejunum Middle	No explicit case or control marker detected.
Unassigned	Unassigned	GSM1708510	No.9_nonIBD_Jejunum_Lower	Biopsy specimen Disease state: NonIBD; Tissue: NonIBD Jejunum Lower	No explicit case or control marker detected.
Unassigned	Unassigned	GSM1708511	No.9_nonIBD_Ileum_Upper	Biopsy specimen Disease state: NonIBD; Tissue: NonIBD Ileum Upper	No explicit case or control marker detected.
Unassigned	Unassigned	GSM1708512	No.9_nonIBD_Ileum_Middle	Biopsy specimen Disease state: NonIBD; Tissue: NonIBD Ileum Middle	No explicit case or control marker detected.
Unassigned	Unassigned	GSM1708513	No.9_nonIBD_colon	Biopsy specimen Disease state: NonIBD; Tissue: NonIBD colon	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.

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Use as Discovery Cohort