GSE133060

Gene expression data from a cohort of Chilean Ulcerative Colitis human intestinal samples

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

8 case / 8 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: 16 samples
Specimen: Tissue
Reported/interpreted study design: Disease/model vs control Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Dubois-Camacho K, Cidlowski J, Díaz-Jimenez D, Microarray Core N
Contact name: NIEHS Microarray Core
Submission date: 2019-06-20
Last update: 2019-10-09
Organization: NIEHS
Department: DIR
Public date: 2019-10-07
Experiment types: Expression profiling by array
Platforms: GPL4133 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Feature Number version)
Series type: SubSeries
SubSeries: Not available
BioProject: PRJNA549861

Summary

Different genes, especially cytokines, have been deregulated in the inflammatory environment of intestinal mucosa in ulcerative colitis patients. The effects of differential gene expression such as immunological factors have been described before, however, there is no evidence of alarmins deregulated by microRNAs impacting on the pathophysiology of UC. Our goal is to study deregulated genes in inflamed mucosa for microRNA pairing in a Chilean cohort of patients. We used microarrays to compare inflamed and non inflamed mucosa from chilean ulcerative colitis patients

Overall design

Inflamed and non inflamed human Intestinal biopsies were obtained in colonoscopy from Ulcerative Colitis patients and we performed gene expresion microarrays to analyze the molecular interaction between them and to determine possible relationships associated to the pathophysiology and clinical presentation

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 16 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	Publication context when PubMed identifiers are already known.	No match found

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

97% DE readiness

Contrast completeness

25/25 pts

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

Minimum group size

20/20 pts

Each contrast group has at least 2 samples.

Processed data availability

20/20 pts

Processed data is marked available in the GEO index.

Sample decision clarity

15/15 pts

All samples are assigned to a case or control group.

Blocking warnings

7/10 pts

Warnings are present, but none are critical blockers.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

Secondary RNA assay context should be analyzed separately from ordinary bulk RNA-seq.

Next Steps

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

Analysis Preparation Checklist

5/6 ready

Group labels reviewed

Needs review

Siftome proposed case and control labels, but no reviewer confirmation is stored yet.

Open the sample grouping CSV and confirm group labels before analysis.

Minimum sample count met

Ready

Both groups meet the minimum of 2 samples.

Confirm whether the cohort is large enough for the intended statistical analysis.

Processed counts available

Ready

Processed data availability is marked true in the GEO index.

Verify that downloaded processed files contain usable count or expression identifiers.

Ambiguous samples handled

Ready

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

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

Exclusion decisions recorded

Ready

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

Record any manual exclusions in the downstream analysis notes.

Source traceability preserved

Ready

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

Keep GEO accessions with exported metadata.

Bioinformatician Review

Bioinformatician review required

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

Analysis readiness has blockers that must be resolved before DE.

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

Why This Is Ranked Here

Tumor vs normal

Not suitable Dataset does not meet the current suitability threshold.

Applied Review Decisions

No active review decisions affect this ranking.

Derived Classifications

Assay differs from search intent Microarray Search intent expects bulk RNA-seq. Assay came from Normalization rules.
Disease context Inflammatory bowel disease, ulcerative colitis Disease context came from Normalization rules.
Likely case group Inflamed tissue 8 samples
Likely control group Non-inflamed tissue 8 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: Tissue. Comparison suitability: 0%.
Interpreted disease metadata: Inflammatory bowel disease, Ulcerative colitis.
Processed data is available for downstream review.

Cautions

Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA 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.
Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
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

69 fields

Field Value Source Derived by Confidence Evidence Reason

assay_type microarray GSE133060 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence microarray dataset_accession: GSE133060 dataset_title: Gene expression data from a cohort of Chilean Ulcerative Colitis human intestinal samples organism: Homo sapiens assay_type: microarr... keyword match keyword match: microarray

disease inflammatory bowel disease GSE133060 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflamed mucosa dataset_accession: GSE133060 dataset_title: Gene expression data from a cohort of Chilean Ulcerative Colitis human intestinal samples organism: Homo sapiens assay_type: microarr... controlled vocabulary controlled vocabulary disease match: inflamed mucosa

disease ulcerative colitis GSE133060 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis dataset_accession: GSE133060 dataset_title: Gene expression data from a cohort of Chilean Ulcerative Colitis human intestinal samples organism: Homo sapiens assay_type: microarr... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease inflammatory bowel disease GSM3899211 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflamed mucosa Inflamed mucosa from UC patient 1 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary disease match: inflamed mucosa

disease ulcerative colitis GSM3899211 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Inflamed mucosa from UC patient 1 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease inflammatory bowel disease GSM3899212 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflamed mucosa Non inflamed mucosa from UC patient 1 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Non Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary disease match: inflamed mucosa

disease ulcerative colitis GSM3899212 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Non inflamed mucosa from UC patient 1 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Non Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease inflammatory bowel disease GSM3899213 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflamed mucosa Inflamed mucosa from UC patient 2 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary disease match: inflamed mucosa

disease ulcerative colitis GSM3899213 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Inflamed mucosa from UC patient 2 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease inflammatory bowel disease GSM3899214 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflamed mucosa Non inflamed mucosa from UC patient 2 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Non Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary disease match: inflamed mucosa

disease ulcerative colitis GSM3899214 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Non inflamed mucosa from UC patient 2 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Non Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease inflammatory bowel disease GSM3899215 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflamed mucosa Inflamed mucosa from UC patient 3 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary disease match: inflamed mucosa

disease ulcerative colitis GSM3899215 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Inflamed mucosa from UC patient 3 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease inflammatory bowel disease GSM3899216 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflamed mucosa Non inflamed mucosa from UC patient 3 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Non Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary disease match: inflamed mucosa

disease ulcerative colitis GSM3899216 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Non inflamed mucosa from UC patient 3 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Non Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease inflammatory bowel disease GSM3899217 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflamed mucosa Inflamed mucosa from UC patient 4 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary disease match: inflamed mucosa

disease ulcerative colitis GSM3899217 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Inflamed mucosa from UC patient 4 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease inflammatory bowel disease GSM3899218 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflamed mucosa Non inflamed mucosa from UC patient 4 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Non Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary disease match: inflamed mucosa

disease ulcerative colitis GSM3899218 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Non inflamed mucosa from UC patient 4 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Non Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease inflammatory bowel disease GSM3899219 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflamed mucosa Inflamed mucosa from UC patient 5 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary disease match: inflamed mucosa

disease ulcerative colitis GSM3899219 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Inflamed mucosa from UC patient 5 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease inflammatory bowel disease GSM3899220 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflamed mucosa Non inflamed mucosa from UC patient 5 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Non Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary disease match: inflamed mucosa

disease ulcerative colitis GSM3899220 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Non inflamed mucosa from UC patient 5 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Non Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease inflammatory bowel disease GSM3899221 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflamed mucosa Inflamed mucosa from UC patient 6 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary disease match: inflamed mucosa

disease ulcerative colitis GSM3899221 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Inflamed mucosa from UC patient 6 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease inflammatory bowel disease GSM3899222 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflamed mucosa Non inflamed mucosa from UC patient 6 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Non Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary disease match: inflamed mucosa

disease ulcerative colitis GSM3899222 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Non inflamed mucosa from UC patient 6 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Non Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease inflammatory bowel disease GSM3899223 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflamed mucosa Inflamed mucosa from UC patient 7 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Inflamed; mayo score: 3 controlled vocabulary controlled vocabulary disease match: inflamed mucosa

disease ulcerative colitis GSM3899223 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Inflamed mucosa from UC patient 7 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Inflamed; mayo score: 3 controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease inflammatory bowel disease GSM3899224 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflamed mucosa Non inflamed mucosa from UC patient 7 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Non Inflamed; mayo score: 3 controlled vocabulary controlled vocabulary disease match: inflamed mucosa

disease ulcerative colitis GSM3899224 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Non inflamed mucosa from UC patient 7 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Non Inflamed; mayo score: 3 controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease inflammatory bowel disease GSM3899225 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflamed mucosa Inflamed mucosa from UC patient 8 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary disease match: inflamed mucosa

disease ulcerative colitis GSM3899225 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Inflamed mucosa from UC patient 8 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease inflammatory bowel disease GSM3899226 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflamed mucosa Non inflamed mucosa from UC patient 8 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Non Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary disease match: inflamed mucosa

disease ulcerative colitis GSM3899226 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Non inflamed mucosa from UC patient 8 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Non Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary disease match: ulcerative colitis

organism Homo sapiens GSE133060 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE133060 dataset_title: Gene expression data from a cohort of Chilean Ulcerative Colitis human intestinal samples organism: Homo sapiens assay_type: microarr... keyword match keyword match: homo sapiens

sample_type inflamed tissue GSM3899211 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed Inflamed mucosa from UC patient 1 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type non-inflamed tissue GSM3899212 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence non inflamed Non inflamed mucosa from UC patient 1 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Non Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary sample type match: non inflamed

sample_type inflamed tissue GSM3899213 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed Inflamed mucosa from UC patient 2 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type non-inflamed tissue GSM3899214 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence non inflamed Non inflamed mucosa from UC patient 2 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Non Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary sample type match: non inflamed

sample_type inflamed tissue GSM3899215 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed Inflamed mucosa from UC patient 3 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type non-inflamed tissue GSM3899216 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence non inflamed Non inflamed mucosa from UC patient 3 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Non Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary sample type match: non inflamed

sample_type inflamed tissue GSM3899217 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed Inflamed mucosa from UC patient 4 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type non-inflamed tissue GSM3899218 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence non inflamed Non inflamed mucosa from UC patient 4 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Non Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary sample type match: non inflamed

sample_type inflamed tissue GSM3899219 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed Inflamed mucosa from UC patient 5 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type non-inflamed tissue GSM3899220 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence non inflamed Non inflamed mucosa from UC patient 5 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Non Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary sample type match: non inflamed

sample_type inflamed tissue GSM3899221 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed Inflamed mucosa from UC patient 6 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type non-inflamed tissue GSM3899222 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence non inflamed Non inflamed mucosa from UC patient 6 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Non Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary sample type match: non inflamed

sample_type inflamed tissue GSM3899223 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed Inflamed mucosa from UC patient 7 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Inflamed; mayo score: 3 controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type non-inflamed tissue GSM3899224 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence non inflamed Non inflamed mucosa from UC patient 7 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Non Inflamed; mayo score: 3 controlled vocabulary controlled vocabulary sample type match: non inflamed

sample_type inflamed tissue GSM3899225 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed Inflamed mucosa from UC patient 8 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type non-inflamed tissue GSM3899226 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence non inflamed Non inflamed mucosa from UC patient 8 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Non Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary sample type match: non inflamed

tissue intestine GSE133060 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal dataset_accession: GSE133060 dataset_title: Gene expression data from a cohort of Chilean Ulcerative Colitis human intestinal samples organism: Homo sapiens assay_type: microarr... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM3899211 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal Inflamed mucosa from UC patient 1 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM3899212 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal Non inflamed mucosa from UC patient 1 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Non Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM3899213 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal Inflamed mucosa from UC patient 2 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM3899214 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal Non inflamed mucosa from UC patient 2 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Non Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM3899215 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal Inflamed mucosa from UC patient 3 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM3899216 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal Non inflamed mucosa from UC patient 3 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Non Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM3899217 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal Inflamed mucosa from UC patient 4 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM3899218 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal Non inflamed mucosa from UC patient 4 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Non Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM3899219 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal Inflamed mucosa from UC patient 5 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM3899220 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal Non inflamed mucosa from UC patient 5 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Non Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM3899221 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal Inflamed mucosa from UC patient 6 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM3899222 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal Non inflamed mucosa from UC patient 6 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Non Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM3899223 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal Inflamed mucosa from UC patient 7 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Inflamed; mayo score: 3 controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM3899224 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal Non inflamed mucosa from UC patient 7 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Non Inflamed; mayo score: 3 controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM3899225 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal Inflamed mucosa from UC patient 8 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary tissue match: intestinal

tissue intestine GSM3899226 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal Non inflamed mucosa from UC patient 8 Intestinal mucosal biopsies diagnosis: Ulcerative Colitis; tissue: Intestinal mucosal biopsies; inflammation: Non Inflamed; mayo score: 2 controlled vocabulary controlled vocabulary tissue match: intestinal

Sample Group Preview

16 rows shown Show Hide

Study totals: Case 8 | Control 8 | Unassigned 0 | Excluded 0 | Ambiguous 0 16 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Inflamed tissue	Case	GSM3899211	Inflamed mucosa from UC patient 1	Intestinal mucosal biopsies Diagnosis: Ulcerative Colitis; Tissue: Intestinal mucosal biopsies; Inflammation: Inflamed; Mayo score: 2	Explicit sample label case marker detected.
Inflamed tissue	Case	GSM3899213	Inflamed mucosa from UC patient 2	Intestinal mucosal biopsies Diagnosis: Ulcerative Colitis; Tissue: Intestinal mucosal biopsies; Inflammation: Inflamed; Mayo score: 2	Explicit sample label case marker detected.
Inflamed tissue	Case	GSM3899215	Inflamed mucosa from UC patient 3	Intestinal mucosal biopsies Diagnosis: Ulcerative Colitis; Tissue: Intestinal mucosal biopsies; Inflammation: Inflamed; Mayo score: 2	Explicit sample label case marker detected.
Inflamed tissue	Case	GSM3899217	Inflamed mucosa from UC patient 4	Intestinal mucosal biopsies Diagnosis: Ulcerative Colitis; Tissue: Intestinal mucosal biopsies; Inflammation: Inflamed; Mayo score: 2	Explicit sample label case marker detected.
Inflamed tissue	Case	GSM3899219	Inflamed mucosa from UC patient 5	Intestinal mucosal biopsies Diagnosis: Ulcerative Colitis; Tissue: Intestinal mucosal biopsies; Inflammation: Inflamed; Mayo score: 2	Explicit sample label case marker detected.
Inflamed tissue	Case	GSM3899221	Inflamed mucosa from UC patient 6	Intestinal mucosal biopsies Diagnosis: Ulcerative Colitis; Tissue: Intestinal mucosal biopsies; Inflammation: Inflamed; Mayo score: 2	Explicit sample label case marker detected.
Inflamed tissue	Case	GSM3899223	Inflamed mucosa from UC patient 7	Intestinal mucosal biopsies Diagnosis: Ulcerative Colitis; Tissue: Intestinal mucosal biopsies; Inflammation: Inflamed; Mayo score: 3	Explicit sample label case marker detected.
Inflamed tissue	Case	GSM3899225	Inflamed mucosa from UC patient 8	Intestinal mucosal biopsies Diagnosis: Ulcerative Colitis; Tissue: Intestinal mucosal biopsies; Inflammation: Inflamed; Mayo score: 2	Explicit sample label case marker detected.
Non-inflamed tissue	Control	GSM3899212	Non inflamed mucosa from UC patient 1	Intestinal mucosal biopsies Diagnosis: Ulcerative Colitis; Tissue: Intestinal mucosal biopsies; Inflammation: Non Inflamed; Mayo score: 2	Sample-local control marker detected.
Non-inflamed tissue	Control	GSM3899214	Non inflamed mucosa from UC patient 2	Intestinal mucosal biopsies Diagnosis: Ulcerative Colitis; Tissue: Intestinal mucosal biopsies; Inflammation: Non Inflamed; Mayo score: 2	Sample-local control marker detected.
Non-inflamed tissue	Control	GSM3899216	Non inflamed mucosa from UC patient 3	Intestinal mucosal biopsies Diagnosis: Ulcerative Colitis; Tissue: Intestinal mucosal biopsies; Inflammation: Non Inflamed; Mayo score: 2	Sample-local control marker detected.
Non-inflamed tissue	Control	GSM3899218	Non inflamed mucosa from UC patient 4	Intestinal mucosal biopsies Diagnosis: Ulcerative Colitis; Tissue: Intestinal mucosal biopsies; Inflammation: Non Inflamed; Mayo score: 2	Sample-local control marker detected.
Non-inflamed tissue	Control	GSM3899220	Non inflamed mucosa from UC patient 5	Intestinal mucosal biopsies Diagnosis: Ulcerative Colitis; Tissue: Intestinal mucosal biopsies; Inflammation: Non Inflamed; Mayo score: 2	Sample-local control marker detected.
Non-inflamed tissue	Control	GSM3899222	Non inflamed mucosa from UC patient 6	Intestinal mucosal biopsies Diagnosis: Ulcerative Colitis; Tissue: Intestinal mucosal biopsies; Inflammation: Non Inflamed; Mayo score: 2	Sample-local control marker detected.
Non-inflamed tissue	Control	GSM3899224	Non inflamed mucosa from UC patient 7	Intestinal mucosal biopsies Diagnosis: Ulcerative Colitis; Tissue: Intestinal mucosal biopsies; Inflammation: Non Inflamed; Mayo score: 3	Sample-local control marker detected.
Non-inflamed tissue	Control	GSM3899226	Non inflamed mucosa from UC patient 8	Intestinal mucosal biopsies Diagnosis: Ulcerative Colitis; Tissue: Intestinal mucosal biopsies; Inflammation: Non Inflamed; Mayo score: 2	Sample-local control marker detected.

Use as Discovery Cohort

External Validation Finder

Carry Siftome's disease, organism, specimen, assay, data type, and accession into a validation project. Uncertain fields remain Unknown.