GSE87465

Gene expression profiling of mucosal biopsies from pediatric patients with moderately to severely active ulcerative colitis

Whole-study status Not suitable

Dataset does not meet the current suitability threshold.

Whole-study downloads — these do not apply your sample requirements.

Selected cohort requirements

Samples meeting selected requirements: 0 cases / 0 controls

View matching samples

19 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: 19 samples
Specimen: Biopsy
Reported/interpreted study design: Unclear study design Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Li K, Strauss R, Chan D, Brodmerkel C, Friedman JR
Contact name: K Li
Submission date: 2016-09-29
Last update: 2019-03-02
Organization: Janssen R&D
Department: Not available
Public date: 2018-12-01
Experiment types: Expression profiling by array
Platforms: GPL13158 [HT_HG-U133_Plus_PM] Affymetrix HT HG-U133+ PM Array Plate
Series type: SubSeries
SubSeries: Not available
BioProject: PRJNA344859

Summary

To acquire a better understanding of the molecular pathogenesis of pediatric UC with different disease extent, we performed mRNA microarray studies to compare gene expression of patients with extensive UC vs. that of patients with limited UC. No significant difference was observed in mRNA expression between extensive and limited UC in pediatric patients.

Overall design

Mucosal biopsy samples (13 extensive and 6 limited UC) were collected for RNA extraction and microarray analysis.

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 19 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 Molecular Comparison of Adult and Pediatric Ulcerative Colitis Indicates Broad Similarity of Molecular Pathways in Disease Tissue. Journal of pediatric gastroenterology and nutrition, 2018 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

55% 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

15/15 pts

All samples are assigned to a case or control group.

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.
Critical dataset warnings must be resolved.

Next Steps

Resolve critical warnings before downstream analysis.

Analysis Preparation Checklist

4/6 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

Ready

No review-needed or unassigned samples are present in the proposed grouping.

Review the grouping table for biologically meaningful differences that the automated checks may not detect.

Exclusion decisions recorded

Ready

No hard-excluded samples were detected by the current rules.

Record any manual exclusions in the downstream analysis notes.

Source traceability preserved

Ready

The dataset and sample accessions can be traced back to GEO.

Keep GEO accessions with exported metadata.

Bioinformatician Review

Bioinformatician review required

Ask a bioinformatician to review grouping, count availability, exclusions, and design before DE.

Analysis readiness has blockers that must be resolved before DE.

Analysis preparation checklist contains blocked items.

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

At least one comparison group has fewer than two samples.

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 Ulcerative colitis Disease context came from Normalization rules.
Likely case group Ulcerative colitis 19 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: Ulcerative colitis.
Processed data is available for downstream review.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 29401083.
Publication context: Molecular Comparison of Adult and Pediatric Ulcerative Colitis Indicates Broad Similarity of Molecular Pathways in Disease Tissue.. Journal of pediatric gastroenterology and nutrition, 2018. PMID 29401083. DOI 10.1097/MPG.0000000000001898.

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.
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 microarray cohorts should be compared separately from RNA-seq cohorts.
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.
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.
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

98 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source colon GSM2332079 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: Colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2332080 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: Colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2332081 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: Colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2332082 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: Colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2332083 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: Colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2332084 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: Colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2332085 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: Colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2332086 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: Colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2332087 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: Colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2332088 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: Colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2332089 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: Colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2332090 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: Colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2332091 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: Colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2332092 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: Colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2332093 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: Colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2332094 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: Colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2332095 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: Colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2332096 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: Colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2332097 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: Colon sample-anatomical-source-v1 sample-local anatomical source

assay_type microarray GSE87465 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence microarray dataset_accession: GSE87465 dataset_title: Gene expression profiling of mucosal biopsies from pediatric patients with moderately to severely active ulcerative colitis organism: ... keyword match keyword match: microarray

collection_method biopsy GSM2332079 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Z343899-23 tissue biopsy subject: 52; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 16; tissue: Colon controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM2332080 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy J369887-23 tissue biopsy subject: 23; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 9; tissue: Colon controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM2332081 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy W457462-23 tissue biopsy subject: 39; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 12; tissue: Colon controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM2332082 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy L419087-22 tissue biopsy subject: 53; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 17; tissue: Colon controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM2332083 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Y740511-23 tissue biopsy subject: 48; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 12; tissue: Colon controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM2332084 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Y200913-23 tissue biopsy subject: 35; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 10; tissue: Colon controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM2332085 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy K690175-22 tissue biopsy subject: 49; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 6; tissue: Colon controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM2332086 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy X399843-23 tissue biopsy subject: 36; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 16; tissue: Colon controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM2332087 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy W457491-23 tissue biopsy subject: 22; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 16; tissue: Colon controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM2332088 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Y396214-23 tissue biopsy subject: 42; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 15; tissue: Colon controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM2332089 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy W457483-23 tissue biopsy subject: 31; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 15; tissue: Colon controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM2332090 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy W457453-23 tissue biopsy subject: 19; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 13; tissue: Colon controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM2332091 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy K412777-22 tissue biopsy subject: 50; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 11; tissue: Colon controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM2332092 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy I769988-23 tissue biopsy subject: 37; diseaseextent: LIMITED UC; disease: Ulcerative Colitis (UC); age: 7; tissue: Colon controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM2332093 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy I769929-23 tissue biopsy subject: 20; diseaseextent: LIMITED UC; disease: Ulcerative Colitis (UC); age: 9; tissue: Colon controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM2332094 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy I769897-23 tissue biopsy subject: 38; diseaseextent: LIMITED UC; disease: Ulcerative Colitis (UC); age: 17; tissue: Colon controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM2332095 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy I771787-23 tissue biopsy subject: 18; diseaseextent: LIMITED UC; disease: Ulcerative Colitis (UC); age: 16; tissue: Colon controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM2332096 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Y396209-23 tissue biopsy subject: 51; diseaseextent: LIMITED UC; disease: Ulcerative Colitis (UC); age: 15; tissue: Colon controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM2332097 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Z094865-23 tissue biopsy subject: 56; diseaseextent: LIMITED UC; disease: Ulcerative Colitis (UC); age: 15; tissue: Colon controlled vocabulary controlled vocabulary collection method match: biopsy

disease ulcerative colitis GSE87465 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis dataset_accession: GSE87465 dataset_title: Gene expression profiling of mucosal biopsies from pediatric patients with moderately to severely active ulcerative colitis organism: ... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2332079 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Z343899-23 tissue biopsy subject: 52; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 16; tissue: Colon controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2332080 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis J369887-23 tissue biopsy subject: 23; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 9; tissue: Colon controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2332081 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis W457462-23 tissue biopsy subject: 39; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 12; tissue: Colon controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2332082 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis L419087-22 tissue biopsy subject: 53; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 17; tissue: Colon controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2332083 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Y740511-23 tissue biopsy subject: 48; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 12; tissue: Colon controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2332084 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Y200913-23 tissue biopsy subject: 35; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 10; tissue: Colon controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2332085 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis K690175-22 tissue biopsy subject: 49; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 6; tissue: Colon controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2332086 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis X399843-23 tissue biopsy subject: 36; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 16; tissue: Colon controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2332087 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis W457491-23 tissue biopsy subject: 22; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 16; tissue: Colon controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2332088 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Y396214-23 tissue biopsy subject: 42; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 15; tissue: Colon controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2332089 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis W457483-23 tissue biopsy subject: 31; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 15; tissue: Colon controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2332090 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis W457453-23 tissue biopsy subject: 19; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 13; tissue: Colon controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2332091 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis K412777-22 tissue biopsy subject: 50; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 11; tissue: Colon controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2332092 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis I769988-23 tissue biopsy subject: 37; diseaseextent: LIMITED UC; disease: Ulcerative Colitis (UC); age: 7; tissue: Colon controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2332093 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis I769929-23 tissue biopsy subject: 20; diseaseextent: LIMITED UC; disease: Ulcerative Colitis (UC); age: 9; tissue: Colon controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2332094 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis I769897-23 tissue biopsy subject: 38; diseaseextent: LIMITED UC; disease: Ulcerative Colitis (UC); age: 17; tissue: Colon controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2332095 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis I771787-23 tissue biopsy subject: 18; diseaseextent: LIMITED UC; disease: Ulcerative Colitis (UC); age: 16; tissue: Colon controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2332096 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Y396209-23 tissue biopsy subject: 51; diseaseextent: LIMITED UC; disease: Ulcerative Colitis (UC); age: 15; tissue: Colon controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM2332097 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Z094865-23 tissue biopsy subject: 56; diseaseextent: LIMITED UC; disease: Ulcerative Colitis (UC); age: 15; tissue: Colon controlled vocabulary controlled vocabulary disease match: ulcerative colitis

organism Homo sapiens GSE87465 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE87465 dataset_title: Gene expression profiling of mucosal biopsies from pediatric patients with moderately to severely active ulcerative colitis organism: ... keyword match keyword match: homo sapiens

primary_tissue primary tissue GSM2332079 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Z343899-23 tissue biopsy subject: 52; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 16; tissue: Colon controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM2332080 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy J369887-23 tissue biopsy subject: 23; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 9; tissue: Colon controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM2332081 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy W457462-23 tissue biopsy subject: 39; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 12; tissue: Colon controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM2332082 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy L419087-22 tissue biopsy subject: 53; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 17; tissue: Colon controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM2332083 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Y740511-23 tissue biopsy subject: 48; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 12; tissue: Colon controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM2332084 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Y200913-23 tissue biopsy subject: 35; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 10; tissue: Colon controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM2332085 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy K690175-22 tissue biopsy subject: 49; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 6; tissue: Colon controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM2332086 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy X399843-23 tissue biopsy subject: 36; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 16; tissue: Colon controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM2332087 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy W457491-23 tissue biopsy subject: 22; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 16; tissue: Colon controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM2332088 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Y396214-23 tissue biopsy subject: 42; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 15; tissue: Colon controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM2332089 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy W457483-23 tissue biopsy subject: 31; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 15; tissue: Colon controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM2332090 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy W457453-23 tissue biopsy subject: 19; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 13; tissue: Colon controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM2332091 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy K412777-22 tissue biopsy subject: 50; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 11; tissue: Colon controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM2332092 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy I769988-23 tissue biopsy subject: 37; diseaseextent: LIMITED UC; disease: Ulcerative Colitis (UC); age: 7; tissue: Colon controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM2332093 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy I769929-23 tissue biopsy subject: 20; diseaseextent: LIMITED UC; disease: Ulcerative Colitis (UC); age: 9; tissue: Colon controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM2332094 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy I769897-23 tissue biopsy subject: 38; diseaseextent: LIMITED UC; disease: Ulcerative Colitis (UC); age: 17; tissue: Colon controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM2332095 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy I771787-23 tissue biopsy subject: 18; diseaseextent: LIMITED UC; disease: Ulcerative Colitis (UC); age: 16; tissue: Colon controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM2332096 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Y396209-23 tissue biopsy subject: 51; diseaseextent: LIMITED UC; disease: Ulcerative Colitis (UC); age: 15; tissue: Colon controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM2332097 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Z094865-23 tissue biopsy subject: 56; diseaseextent: LIMITED UC; disease: Ulcerative Colitis (UC); age: 15; tissue: Colon controlled vocabulary controlled vocabulary primary tissue match: biopsy

tissue colon GSM2332079 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Z343899-23 tissue biopsy subject: 52; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 16; tissue: Colon controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2332080 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon J369887-23 tissue biopsy subject: 23; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 9; tissue: Colon controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2332081 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon W457462-23 tissue biopsy subject: 39; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 12; tissue: Colon controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2332082 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon L419087-22 tissue biopsy subject: 53; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 17; tissue: Colon controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2332083 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Y740511-23 tissue biopsy subject: 48; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 12; tissue: Colon controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2332084 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Y200913-23 tissue biopsy subject: 35; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 10; tissue: Colon controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2332085 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon K690175-22 tissue biopsy subject: 49; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 6; tissue: Colon controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2332086 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon X399843-23 tissue biopsy subject: 36; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 16; tissue: Colon controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2332087 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon W457491-23 tissue biopsy subject: 22; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 16; tissue: Colon controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2332088 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Y396214-23 tissue biopsy subject: 42; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 15; tissue: Colon controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2332089 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon W457483-23 tissue biopsy subject: 31; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 15; tissue: Colon controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2332090 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon W457453-23 tissue biopsy subject: 19; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 13; tissue: Colon controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2332091 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon K412777-22 tissue biopsy subject: 50; diseaseextent: EXTENSIVE; disease: Ulcerative Colitis (UC); age: 11; tissue: Colon controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2332092 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon I769988-23 tissue biopsy subject: 37; diseaseextent: LIMITED UC; disease: Ulcerative Colitis (UC); age: 7; tissue: Colon controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2332093 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon I769929-23 tissue biopsy subject: 20; diseaseextent: LIMITED UC; disease: Ulcerative Colitis (UC); age: 9; tissue: Colon controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2332094 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon I769897-23 tissue biopsy subject: 38; diseaseextent: LIMITED UC; disease: Ulcerative Colitis (UC); age: 17; tissue: Colon controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2332095 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon I771787-23 tissue biopsy subject: 18; diseaseextent: LIMITED UC; disease: Ulcerative Colitis (UC); age: 16; tissue: Colon controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2332096 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Y396209-23 tissue biopsy subject: 51; diseaseextent: LIMITED UC; disease: Ulcerative Colitis (UC); age: 15; tissue: Colon controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2332097 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Z094865-23 tissue biopsy subject: 56; diseaseextent: LIMITED UC; disease: Ulcerative Colitis (UC); age: 15; tissue: Colon controlled vocabulary controlled vocabulary tissue match: colon

Sample Group Preview

19 rows shown Show Hide

Study totals: Case 19 | Control 0 | Unassigned 0 | Excluded 0 | Ambiguous 0 19 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Ulcerative colitis	Case	GSM2332079	Z343899-23	Tissue biopsy Subject: 52; Diseaseextent: EXTENSIVE; Disease: Ulcerative Colitis (UC); Age: 16; Tissue: Colon	Case marker detected.
Ulcerative colitis	Case	GSM2332080	J369887-23	Tissue biopsy Subject: 23; Diseaseextent: EXTENSIVE; Disease: Ulcerative Colitis (UC); Age: 9; Tissue: Colon	Case marker detected.
Ulcerative colitis	Case	GSM2332081	W457462-23	Tissue biopsy Subject: 39; Diseaseextent: EXTENSIVE; Disease: Ulcerative Colitis (UC); Age: 12; Tissue: Colon	Case marker detected.
Ulcerative colitis	Case	GSM2332082	L419087-22	Tissue biopsy Subject: 53; Diseaseextent: EXTENSIVE; Disease: Ulcerative Colitis (UC); Age: 17; Tissue: Colon	Case marker detected.
Ulcerative colitis	Case	GSM2332083	Y740511-23	Tissue biopsy Subject: 48; Diseaseextent: EXTENSIVE; Disease: Ulcerative Colitis (UC); Age: 12; Tissue: Colon	Case marker detected.
Ulcerative colitis	Case	GSM2332084	Y200913-23	Tissue biopsy Subject: 35; Diseaseextent: EXTENSIVE; Disease: Ulcerative Colitis (UC); Age: 10; Tissue: Colon	Case marker detected.
Ulcerative colitis	Case	GSM2332085	K690175-22	Tissue biopsy Subject: 49; Diseaseextent: EXTENSIVE; Disease: Ulcerative Colitis (UC); Age: 6; Tissue: Colon	Case marker detected.
Ulcerative colitis	Case	GSM2332086	X399843-23	Tissue biopsy Subject: 36; Diseaseextent: EXTENSIVE; Disease: Ulcerative Colitis (UC); Age: 16; Tissue: Colon	Case marker detected.
Ulcerative colitis	Case	GSM2332087	W457491-23	Tissue biopsy Subject: 22; Diseaseextent: EXTENSIVE; Disease: Ulcerative Colitis (UC); Age: 16; Tissue: Colon	Case marker detected.
Ulcerative colitis	Case	GSM2332088	Y396214-23	Tissue biopsy Subject: 42; Diseaseextent: EXTENSIVE; Disease: Ulcerative Colitis (UC); Age: 15; Tissue: Colon	Case marker detected.
Ulcerative colitis	Case	GSM2332089	W457483-23	Tissue biopsy Subject: 31; Diseaseextent: EXTENSIVE; Disease: Ulcerative Colitis (UC); Age: 15; Tissue: Colon	Case marker detected.
Ulcerative colitis	Case	GSM2332090	W457453-23	Tissue biopsy Subject: 19; Diseaseextent: EXTENSIVE; Disease: Ulcerative Colitis (UC); Age: 13; Tissue: Colon	Case marker detected.
Ulcerative colitis	Case	GSM2332091	K412777-22	Tissue biopsy Subject: 50; Diseaseextent: EXTENSIVE; Disease: Ulcerative Colitis (UC); Age: 11; Tissue: Colon	Case marker detected.
Ulcerative colitis	Case	GSM2332092	I769988-23	Tissue biopsy Subject: 37; Diseaseextent: LIMITED UC; Disease: Ulcerative Colitis (UC); Age: 7; Tissue: Colon	Case marker detected.
Ulcerative colitis	Case	GSM2332093	I769929-23	Tissue biopsy Subject: 20; Diseaseextent: LIMITED UC; Disease: Ulcerative Colitis (UC); Age: 9; Tissue: Colon	Case marker detected.
Ulcerative colitis	Case	GSM2332094	I769897-23	Tissue biopsy Subject: 38; Diseaseextent: LIMITED UC; Disease: Ulcerative Colitis (UC); Age: 17; Tissue: Colon	Case marker detected.
Ulcerative colitis	Case	GSM2332095	I771787-23	Tissue biopsy Subject: 18; Diseaseextent: LIMITED UC; Disease: Ulcerative Colitis (UC); Age: 16; Tissue: Colon	Case marker detected.
Ulcerative colitis	Case	GSM2332096	Y396209-23	Tissue biopsy Subject: 51; Diseaseextent: LIMITED UC; Disease: Ulcerative Colitis (UC); Age: 15; Tissue: Colon	Case marker detected.
Ulcerative colitis	Case	GSM2332097	Z094865-23	Tissue biopsy Subject: 56; Diseaseextent: LIMITED UC; Disease: Ulcerative Colitis (UC); Age: 15; Tissue: Colon	Case marker detected.

Use as Discovery Cohort

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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