GSE37283

Gene Expression Changes in Non-Dysplastic Mucosa from Patients with Ulcerative Colitis Harboring Remote Neoplastic Lesions

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

15 case / 5 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: 20 samples
Specimen: Tissue
Reported/interpreted study design: Disease/model vs control Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Pekow J, Dougherty U, Huang Y, Gometz E, Nathanson J, Cohen G, Levy S, Kocherginsky M, Venu N, Westerhoff M, Hart J, Noffsinger AE, Hanauer S, Hurst RD, Fichera A, Joseph LJ, Liu Q, Bissonnette M
Contact name: Yong Huang
Submission date: 2012-04-16
Last update: 2020-02-07
Organization: University of Chicago
Department: Medicine
Public date: 2012-04-20
Experiment types: Expression profiling by array
Platforms: GPL13158 [HT_HG-U133_Plus_PM] Affymetrix HT HG-U133+ PM Array Plate
Series type: Series
SubSeries: Not available
BioProject: PRJNA159399

Summary

Background and Aims: Individuals with ulcerative colitis (UC) are at increased risk for colorectal cancer, although underlying mechanisms are incompletely understood. We sought to identify a potential gene expression signature in non-dysplastic distal mucosa that as a “genetic field effect” could be a marker for remote neoplastic lesions. Results: 468 genes were significantly up-regulated and 541 genes were significantly down-regulated >2-fold in UC patients with neoplasia compared to UC patients without neoplasia. Nine genes (ACSL1, BIRC3, CLC, CREM, ELTD1, FGG, S100A9, THBD, and TPD52L1) were progressively and significantly up-regulated from controls to quiescent non-dysplastic UC to UC with neoplasia. Immunostaining of proteins revealed increases in tissue expression of S100A9 and REG1 in UC-associated cancer and in non-dysplastic tissue from UC patients harboring remote neoplasia, compared to UC patients without dysplasia and normal controls. Conclusions: Gene expression changes occur as a field effect in UC patients without active inflammation who harbor a remote dysplastic lesion. Further characterization of these genes and proteins might elucidate pathways of carcinogenesis in IBD and lead to the development of more accurate, less invasive markers of dysplasia in those at increased risk.

Overall design

Microarray assay were conducted on 20 RNA samples isolated from colon mucosa of 20 patients. Of these patients, 5 were normal controls, 4 had quiescent UC, and 11 had UC with neoplasia. Patients were included if they had a previous clinical diagnosis of UC confirmed by an expert GI pathologist, a disease duration > 7 years, and an extent of disease >20 cm proximal to the anal verge.

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 20 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. 4 linked publications 4 DOIs Primary publication Gene signature distinguishes patients with chronic ulcerative colitis harboring remote neoplastic lesions. Inflammatory bowel diseases, 2013 PubMed DOI Intestinal epithelial vitamin D receptor signaling inhibits experimental colitis. The Journal of clinical investigation, 2013 PubMed DOI Related publications Screening of characteristic genes in ulcerative colitis by integrating gene expression profiles. BMC gastroenterology, 2021 PubMed DOI Unraveling Crucial Mitochondria-Related Genes in the Transition from Ulcerative Colitis to Colorectal Cancer. Drug design, development and therapy, 2024 PubMed DOI	Available

Metadata Quality Components

Persisted metadata quality

100 pts

Clarity: 100%
Weight: 100 pts

Sample source clarity: All samples have source metadata and clear GSE/GSM accessions. Group clarity: Rule-based grouping found both case and control samples. Disease clarity: Disease or condition metadata normalized. Tissue clarity: Anatomical source metadata normalized. Treatment clarity: No unclear treatment split detected in the sample metadata. Replicate clarity: No pooled sample or technical replicate flags detected. Data availability clarity: Dataset-level processed or raw data availability is explicit.

Analysis Readiness

Ready after review

97% DE readiness

Contrast completeness

25/25 pts

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

Minimum group size

20/20 pts

Each contrast group has at least 2 samples.

Processed data availability

20/20 pts

Processed data is marked available in the GEO index.

Sample decision clarity

15/15 pts

All samples are assigned to a case or control group.

Blocking warnings

7/10 pts

Warnings are present, but none are critical blockers.

Metadata normalization

10/10 pts

Metadata quality is high enough to support downstream handoff.

Blockers

No readiness blockers detected.

Next Steps

Verify the proposed sample assignments and case-versus-control comparison against the GEO metadata before using them in DESeq2 or another differential-expression tool.
Confirm processed count files and sample identifiers match the exported metadata.

Analysis Preparation Checklist

5/6 ready

Group labels reviewed

Needs review

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

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

Minimum sample count met

Ready

Both groups meet the minimum of 2 samples.

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

Processed counts available

Ready

Processed data availability is marked true in the GEO index.

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

Ambiguous samples handled

Ready

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

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

Exclusion decisions recorded

Ready

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

Record any manual exclusions in the downstream analysis notes.

Source traceability preserved

Ready

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

Keep GEO accessions with exported metadata.

Bioinformatician Review

Bioinformatician review required

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

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

Why This Is Ranked Here

Tumor vs normal

Not suitable Dataset does not meet the current suitability threshold.

Applied Review Decisions

No active review decisions affect this ranking.

Derived Classifications

Assay differs from search intent Microarray Search intent expects bulk RNA-seq. Assay came from Normalization rules.
Disease context Colorectal cancer, inflammatory bowel disease, ulcerative colitis Disease context came from Normalization rules.
Likely case group Ulcerative colitis 15 samples
Likely control group Healthy control 5 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: Colorectal cancer, Inflammatory bowel disease, Ulcerative colitis.
Processed data is available for downstream review.
External evidence: PubMed links 4 publications; 4 DOIs available: PMID 23388545, PMID 23945234, PMID 34717557, PMID 39071816.
Publication context: Gene signature distinguishes patients with chronic ulcerative colitis harboring remote neoplastic lesions.. Inflammatory bowel diseases, 2013. PMID 23388545. DOI 10.1097/MIB.0b013e3182802bac.
Publication context: Intestinal epithelial vitamin D receptor signaling inhibits experimental colitis.. The Journal of clinical investigation, 2013. PMID 23945234. DOI 10.1172/JCI65842.
Publication context: Screening of characteristic genes in ulcerative colitis by integrating gene expression profiles.. BMC gastroenterology, 2021. PMID 34717557. DOI 10.1186/s12876-021-01940-0.
Publication context: 1 additional linked PubMed publications are available.

Cautions

Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
Overall score capped because comparison suitability is weak for the selected search intent.
Overall score capped because microarray cohorts should be compared separately from RNA-seq cohorts.
Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

Microarray expression context was detected; compare separately from RNA-seq cohorts.
Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.

Normalized Fields

71 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source colon GSM915451 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon biopsie sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM915452 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon biopsie sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM915453 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon biopsie sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM915454 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon biopsie sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM915455 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon biopsie sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM915456 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon biopsie sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM915457 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon biopsie sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM915458 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon biopsie sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM915459 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon biopsie sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM915460 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon biopsie sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM915461 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon biopsie sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM915462 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon biopsie sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM915463 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon biopsie sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM915464 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon biopsie sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM915465 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon biopsie sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM915466 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon biopsie sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM915467 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon biopsie sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM915468 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon biopsie sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM915469 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon biopsie sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM915470 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon biopsie sample-anatomical-source-v1 sample-local anatomical source

assay_type microarray GSE37283 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence microarray dataset_accession: GSE37283 dataset_title: Gene Expression Changes in Non-Dysplastic Mucosa from Patients with Ulcerative Colitis Harboring Remote Neoplastic Lesions organism: H... keyword match keyword match: microarray

control_type healthy control GSM915455 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence normal control normal control_CTL1 normal control tissue: colon biopsie controlled vocabulary controlled vocabulary control type match: normal control

control_type healthy control GSM915456 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence normal control normal control_CTL2 normal control tissue: colon biopsie controlled vocabulary controlled vocabulary control type match: normal control

control_type healthy control GSM915457 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence normal control normal control_CTL3 normal control tissue: colon biopsie controlled vocabulary controlled vocabulary control type match: normal control

control_type healthy control GSM915458 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence normal control normal control_CTL4 normal control tissue: colon biopsie controlled vocabulary controlled vocabulary control type match: normal control

control_type healthy control GSM915459 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence normal control normal control_CTL5 normal control tissue: colon biopsie controlled vocabulary controlled vocabulary control type match: normal control

disease colorectal cancer GSE37283 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colorectal cancer dataset_accession: GSE37283 dataset_title: Gene Expression Changes in Non-Dysplastic Mucosa from Patients with Ulcerative Colitis Harboring Remote Neoplastic Lesions organism: H... controlled vocabulary controlled vocabulary disease match: colorectal cancer

disease inflammatory bowel disease GSE37283 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ibd dataset_accession: GSE37283 dataset_title: Gene Expression Changes in Non-Dysplastic Mucosa from Patients with Ulcerative Colitis Harboring Remote Neoplastic Lesions organism: H... controlled vocabulary controlled vocabulary disease match: ibd

disease ulcerative colitis GSE37283 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis dataset_accession: GSE37283 dataset_title: Gene Expression Changes in Non-Dysplastic Mucosa from Patients with Ulcerative Colitis Harboring Remote Neoplastic Lesions organism: H... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM915451 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis quiescent ulcerative colitis_UCN1 quiescent ulcerative colitis tissue: colon biopsie controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM915452 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis quiescent ulcerative colitis_UCN2 quiescent ulcerative colitis tissue: colon biopsie controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM915453 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis quiescent ulcerative colitis_UCN3 quiescent ulcerative colitis tissue: colon biopsie controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM915454 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis quiescent ulcerative colitis_UCN4 quiescent ulcerative colitis tissue: colon biopsie controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM915460 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis ulcerative colitis with neoplasia_UCD1 ulcerative colitis with neoplasia tissue: colon biopsie controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM915461 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis ulcerative colitis with neoplasia_UCD3 ulcerative colitis with neoplasia tissue: colon biopsie controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM915462 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis ulcerative colitis with neoplasia_UCD4 ulcerative colitis with neoplasia tissue: colon biopsie controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM915463 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis ulcerative colitis with neoplasia_UCD6 ulcerative colitis with neoplasia tissue: colon biopsie controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM915464 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis ulcerative colitis with neoplasia_UCD7 ulcerative colitis with neoplasia tissue: colon biopsie controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM915465 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis ulcerative colitis with neoplasia_UCD8 ulcerative colitis with neoplasia tissue: colon biopsie controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM915466 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis ulcerative colitis with neoplasia_UCD9 ulcerative colitis with neoplasia tissue: colon biopsie controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM915467 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis ulcerative colitis with neoplasia_UCD10 ulcerative colitis with neoplasia tissue: colon biopsie controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM915468 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis ulcerative colitis with neoplasia_UCD11 ulcerative colitis with neoplasia tissue: colon biopsie controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM915469 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis ulcerative colitis with neoplasia_UCD12 ulcerative colitis with neoplasia tissue: colon biopsie controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM915470 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis ulcerative colitis with neoplasia_UCD13 ulcerative colitis with neoplasia tissue: colon biopsie controlled vocabulary controlled vocabulary disease match: ulcerative colitis

organism Homo sapiens GSE37283 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE37283 dataset_title: Gene Expression Changes in Non-Dysplastic Mucosa from Patients with Ulcerative Colitis Harboring Remote Neoplastic Lesions organism: H... keyword match keyword match: homo sapiens

sample_type normal tissue GSM915455 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal normal control_CTL1 normal control tissue: colon biopsie controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM915456 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal normal control_CTL2 normal control tissue: colon biopsie controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM915457 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal normal control_CTL3 normal control tissue: colon biopsie controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM915458 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal normal control_CTL4 normal control tissue: colon biopsie controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM915459 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal normal control_CTL5 normal control tissue: colon biopsie controlled vocabulary controlled vocabulary sample type match: normal

tissue colon GSE37283 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon dataset_accession: GSE37283 dataset_title: Gene Expression Changes in Non-Dysplastic Mucosa from Patients with Ulcerative Colitis Harboring Remote Neoplastic Lesions organism: H... controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM915451 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon quiescent ulcerative colitis_UCN1 quiescent ulcerative colitis tissue: colon biopsie controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM915452 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon quiescent ulcerative colitis_UCN2 quiescent ulcerative colitis tissue: colon biopsie controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM915453 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon quiescent ulcerative colitis_UCN3 quiescent ulcerative colitis tissue: colon biopsie controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM915454 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon quiescent ulcerative colitis_UCN4 quiescent ulcerative colitis tissue: colon biopsie controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM915455 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon normal control_CTL1 normal control tissue: colon biopsie controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM915456 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon normal control_CTL2 normal control tissue: colon biopsie controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM915457 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon normal control_CTL3 normal control tissue: colon biopsie controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM915458 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon normal control_CTL4 normal control tissue: colon biopsie controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM915459 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon normal control_CTL5 normal control tissue: colon biopsie controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM915460 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon ulcerative colitis with neoplasia_UCD1 ulcerative colitis with neoplasia tissue: colon biopsie controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM915461 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon ulcerative colitis with neoplasia_UCD3 ulcerative colitis with neoplasia tissue: colon biopsie controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM915462 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon ulcerative colitis with neoplasia_UCD4 ulcerative colitis with neoplasia tissue: colon biopsie controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM915463 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon ulcerative colitis with neoplasia_UCD6 ulcerative colitis with neoplasia tissue: colon biopsie controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM915464 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon ulcerative colitis with neoplasia_UCD7 ulcerative colitis with neoplasia tissue: colon biopsie controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM915465 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon ulcerative colitis with neoplasia_UCD8 ulcerative colitis with neoplasia tissue: colon biopsie controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM915466 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon ulcerative colitis with neoplasia_UCD9 ulcerative colitis with neoplasia tissue: colon biopsie controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM915467 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon ulcerative colitis with neoplasia_UCD10 ulcerative colitis with neoplasia tissue: colon biopsie controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM915468 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon ulcerative colitis with neoplasia_UCD11 ulcerative colitis with neoplasia tissue: colon biopsie controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM915469 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon ulcerative colitis with neoplasia_UCD12 ulcerative colitis with neoplasia tissue: colon biopsie controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM915470 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon ulcerative colitis with neoplasia_UCD13 ulcerative colitis with neoplasia tissue: colon biopsie controlled vocabulary controlled vocabulary tissue match: colon

Sample Group Preview

20 rows shown Show Hide

Study totals: Case 15 | Control 5 | Unassigned 0 | Excluded 0 | Ambiguous 0 20 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Ulcerative colitis	Case	GSM915451	Quiescent ulcerative colitis_UCN1	Quiescent ulcerative colitis Tissue: Colon biopsie	Case marker detected.
Ulcerative colitis	Case	GSM915452	Quiescent ulcerative colitis_UCN2	Quiescent ulcerative colitis Tissue: Colon biopsie	Case marker detected.
Ulcerative colitis	Case	GSM915453	Quiescent ulcerative colitis_UCN3	Quiescent ulcerative colitis Tissue: Colon biopsie	Case marker detected.
Ulcerative colitis	Case	GSM915454	Quiescent ulcerative colitis_UCN4	Quiescent ulcerative colitis Tissue: Colon biopsie	Case marker detected.
Ulcerative colitis	Case	GSM915460	Ulcerative colitis with neoplasia_UCD1	Ulcerative colitis with neoplasia Tissue: Colon biopsie	Case marker detected.
Ulcerative colitis	Case	GSM915461	Ulcerative colitis with neoplasia_UCD3	Ulcerative colitis with neoplasia Tissue: Colon biopsie	Case marker detected.
Ulcerative colitis	Case	GSM915462	Ulcerative colitis with neoplasia_UCD4	Ulcerative colitis with neoplasia Tissue: Colon biopsie	Case marker detected.
Ulcerative colitis	Case	GSM915463	Ulcerative colitis with neoplasia_UCD6	Ulcerative colitis with neoplasia Tissue: Colon biopsie	Case marker detected.
Ulcerative colitis	Case	GSM915464	Ulcerative colitis with neoplasia_UCD7	Ulcerative colitis with neoplasia Tissue: Colon biopsie	Case marker detected.
Ulcerative colitis	Case	GSM915465	Ulcerative colitis with neoplasia_UCD8	Ulcerative colitis with neoplasia Tissue: Colon biopsie	Case marker detected.
Ulcerative colitis	Case	GSM915466	Ulcerative colitis with neoplasia_UCD9	Ulcerative colitis with neoplasia Tissue: Colon biopsie	Case marker detected.
Ulcerative colitis	Case	GSM915467	Ulcerative colitis with neoplasia_UCD10	Ulcerative colitis with neoplasia Tissue: Colon biopsie	Case marker detected.
Ulcerative colitis	Case	GSM915468	Ulcerative colitis with neoplasia_UCD11	Ulcerative colitis with neoplasia Tissue: Colon biopsie	Case marker detected.
Ulcerative colitis	Case	GSM915469	Ulcerative colitis with neoplasia_UCD12	Ulcerative colitis with neoplasia Tissue: Colon biopsie	Case marker detected.
Ulcerative colitis	Case	GSM915470	Ulcerative colitis with neoplasia_UCD13	Ulcerative colitis with neoplasia Tissue: Colon biopsie	Case marker detected.
Healthy control	Control	GSM915455	Normal control_CTL1	Normal control Tissue: Colon biopsie	Sample-local control marker detected.
Healthy control	Control	GSM915456	Normal control_CTL2	Normal control Tissue: Colon biopsie	Sample-local control marker detected.
Healthy control	Control	GSM915457	Normal control_CTL3	Normal control Tissue: Colon biopsie	Sample-local control marker detected.
Healthy control	Control	GSM915458	Normal control_CTL4	Normal control Tissue: Colon biopsie	Sample-local control marker detected.
Healthy control	Control	GSM915459	Normal control_CTL5	Normal control Tissue: Colon biopsie	Sample-local control marker detected.

Use as Discovery Cohort

External Validation Finder

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

Summary

Overall design

Source Evidence

Primary publication

Related publications

Metadata Quality Components

Analysis Readiness

Blockers

Next Steps

Analysis Preparation Checklist

Bioinformatician Review

Why This Is Ranked Here

Applied Review Decisions

Derived Classifications

Intent Interpretation

Ranking Facts

Supporting evidence

Cautions

Dataset Warnings

Normalized Fields

Sample Group Preview

Use as Discovery Cohort