GSE130038

Elevated colonic mucin expression correlates with extended time to surgery for ulcerative colitis patients

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

26 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: bulk RNA-seq
Organism: Homo sapiens
Whole-study samples: 26 samples
Specimen: Tissue
Reported/interpreted study design: Unclear study design Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Eshelman MA, Koltun WA, Yochum GS, Imamura Kawasawa Y
Contact name: Yuka Imamura Kawasawa
Submission date: 2019-04-18
Last update: 2020-07-18
Organization: Penn State University
Department: College of Medicine, Pharmacology
Public date: 2020-04-18
Experiment types: Expression profiling by high throughput sequencing
Platforms: GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Series type: Series
SubSeries: Not available
BioProject: PRJNA533627

Summary

Background: Ulcerative colitis (UC) develops from chronic inflammation of the colon. Most patients respond favorably to medical management, however around 25% of UC patients will require surgery to treat their disease. While surgery is the only curative treatment for UC, it can carry its own risks, particularly when the surgery is emergent. Time from diagnosis to surgery varies dramatically amongst UC patients, thus a better understanding of how the colonic microenvironment relates to disease severity is needed to improve patient outcomes. Methods: We conducted RNA-seq on full-thickness sigmoid colonic tissues from 26 UC patients undergoing colectomy for their disease. Hierarchical clustering of the transcriptomes identified disease subsets. Subsets were characterized using differential gene expression analysis, cell type deconvolution, and network analysis. Results: We identified two distinct UC subsets in our cohort that were distinguished by 957 differentially expressed genes. Cluster 1 was enriched in genes associated with intestinal epithelial cell differentiation, while cluster 2 was enriched in genes associated with epithelial-to-mesenchymal transition and inflammatory responses. Cluster 1 was associated with an extended time from UC diagnosis to colectomy. Of cluster 1 genes, elevated MUC5B, MUC4, and MUC2 expression displayed the strongest correlation with increased time to surgery. Conclusion: Our transcriptome analysis indicates that UC can be subclassified into at least two distinct molecular signatures. We find that elevated mucin gene expression correlates with prolonged time to colectomy after diagnosis. These results identified MUC5B, MUC4, and MUC2 as potential prognostic indicators of disease severity, as reflected in time to surgery.

Overall design

Gene expression profiles from the surgically resected, diseased, sigmoid colon tissue of 26 ulcerative colitis patients were generated by deep sequencing.

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 26 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 Elevated Colonic Mucin Expression Correlates with Extended Time to Surgery for Ulcerative Colitis Patients. Journal of gastrointestinal and liver diseases : JGLD, 2019 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.

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

Disease context Ulcerative colitis Disease context came from Normalization rules.
Likely case group Ulcerative colitis 26 samples
Likely control group No control group detected 0 samples

Intent Interpretation

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

Ranking Facts

Supporting evidence

Prioritized assay: bulk RNA-seq is the active assay expectation.
Interpreted disease metadata: Ulcerative colitis.
Processed data is available for downstream review.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 31826065.
Publication context: Elevated Colonic Mucin Expression Correlates with Extended Time to Surgery for Ulcerative Colitis Patients.. Journal of gastrointestinal and liver diseases : JGLD, 2019. PMID 31826065. DOI 10.15403/jgld-250.

Cautions

Comparison: Unclear study design. Specimen: Tissue. Comparison suitability: 0%.
Downgraded for tissue search because study design or specimen source is unclear.
Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
Missing or unclear metadata. Unclear study design downgraded for patient tissue tumor-vs-normal search intent.
Overall score capped because comparison suitability is weak for the selected search intent.
Missing or unclear metadata. Comparison - Unclear study design. Specimen - Tissue. 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.
Patient-tissue tumor-normal intent requires clear tumor-normal grouping.

Normalized Fields

83 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source colon GSM3730677 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: sigmoid colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM3730678 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: sigmoid colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM3730679 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: sigmoid colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM3730680 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: sigmoid colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM3730681 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: sigmoid colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM3730682 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: sigmoid colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM3730683 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: sigmoid colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM3730684 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: sigmoid colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM3730685 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: sigmoid colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM3730686 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: sigmoid colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM3730687 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: sigmoid colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM3730688 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: sigmoid colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM3730689 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: sigmoid colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM3730690 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: sigmoid colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM3730691 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: sigmoid colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM3730692 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: sigmoid colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM3730693 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: sigmoid colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM3730694 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: sigmoid colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM3730695 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: sigmoid colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM3730696 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: sigmoid colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM3730697 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: sigmoid colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM3730698 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: sigmoid colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM3730699 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: sigmoid colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM3730700 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: sigmoid colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM3730701 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: sigmoid colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM3730702 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: sigmoid colon sample-anatomical-source-v1 sample-local anatomical source

assay_type bulk RNA-seq GSE130038 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence bulk rna-seq dataset_accession: GSE130038 dataset_title: Elevated colonic mucin expression correlates with extended time to surgery for ulcerative colitis patients organism: Homo sapiens ass... keyword match keyword match: bulk rna-seq

disease ulcerative colitis GSE130038 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis dataset_accession: GSE130038 dataset_title: Elevated colonic mucin expression correlates with extended time to surgery for ulcerative colitis patients organism: Homo sapiens ass... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM3730677 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC G155-01 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Male; smoking history: ex smoker; age at diagnosis: 34.86; age at surgery: 37.00; bmi: 25.30 controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM3730678 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC G155-02 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Female; smoking history: Never Smoked; age at diagnosis: 43.76; age at surgery: 54.96; bmi: 34.10 controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM3730679 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC G155-03 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Male; smoking history: Never Smoked; age at diagnosis: 77.52; age at surgery: 80.00; bmi: 25.80 controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM3730680 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC G155-04 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Male; smoking history: ex smoker; age at diagnosis: 54.89; age at surgery: 56.86; bmi: 26.10 controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM3730681 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC G155-05 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Female; smoking history: ex smoker; age at diagnosis: 64.58; age at surgery: 67.00; bmi: 22.90 controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM3730682 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC G155-06 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Female; smoking history: ex smoker; age at diagnosis: 47.55; age at surgery: 57.00; bmi: 20.40 controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM3730683 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC G155-07 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Female; smoking history: ex smoker; age at diagnosis: 50.80; age at surgery: 75.47; bmi: 28.12 controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM3730684 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC G155-08 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Male; smoking history: ex smoker; age at diagnosis: 26.50; age at surgery: 32.13; bmi: 26.85 controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM3730685 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC G155-09 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Female; smoking history: ex smoker; age at diagnosis: 65.01; age at surgery: 66.62; bmi: 30.00 controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM3730686 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC G155-10 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Female; smoking history: ex smoker; age at diagnosis: 48.02; age at surgery: 54.34; bmi: 27.00 controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM3730687 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC G155-11 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Female; smoking history: Never Smoked; age at diagnosis: 31.89; age at surgery: 33.55; bmi: 22.30 controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM3730688 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC G155-12 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Female; smoking history: ex smoker; age at diagnosis: 29.73; age at surgery: 45.00; bmi: 26.99 controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM3730689 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC G155-13 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Male; smoking history: ex smoker; age at diagnosis: 30.39; age at surgery: 40.15; bmi: 35.80 controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM3730690 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC G155-14 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Female; smoking history: Never Smoked; age at diagnosis: 33.30; age at surgery: 36.00; bmi: 37.37 controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM3730691 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC G155-15 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Female; smoking history: Never Smoked; age at diagnosis: 28.97; age at surgery: 36.71; bmi: 21.08 controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM3730692 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC G155-16 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Male; smoking history: ex smoker; age at diagnosis: 71.80; age at surgery: 73.93; bmi: 28.23 controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM3730693 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC G155-17 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Male; smoking history: Never Smoked; age at diagnosis: 55.61; age at surgery: 59.63; bmi: 28.87 controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM3730694 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC G155-18 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Male; smoking history: ex smoker; age at diagnosis: 61.86; age at surgery: 64.13; bmi: 19.80 controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM3730695 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC G155-19 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Male; smoking history: Never Smoked; age at diagnosis: 38.69; age at surgery: 40.00; bmi: 24.91 controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM3730696 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC G155-20 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Male; smoking history: ex smoker; age at diagnosis: 51.58; age at surgery: 53.58; bmi: 26.87 controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM3730697 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC G155-22 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Male; smoking history: Never Smoked; age at diagnosis: 39.82; age at surgery: 45.46; bmi: 31.06 controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM3730698 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC G155-23 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Female; smoking history: Never Smoked; age at diagnosis: 28.87; age at surgery: 41.57; bmi: 21.39 controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM3730699 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC G155-24 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Female; smoking history: ex smoker; age at diagnosis: 20.85; age at surgery: 37.00; bmi: 20.00 controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM3730700 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC G155-25 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Male; smoking history: ex smoker; age at diagnosis: 37.01; age at surgery: 43.20; bmi: 25.80 controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM3730701 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC G155-26 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Male; smoking history: Never Smoked; age at diagnosis: 27.76; age at surgery: 48.74; bmi: 34.01 controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM3730702 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC G155-27 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Male; smoking history: ex smoker; age at diagnosis: 72.66; age at surgery: 75.01; bmi: 22.07 controlled vocabulary controlled vocabulary disease match: UC

organism Homo sapiens GSE130038 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE130038 dataset_title: Elevated colonic mucin expression correlates with extended time to surgery for ulcerative colitis patients organism: Homo sapiens ass... keyword match keyword match: homo sapiens

tissue colon GSE130038 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon dataset_accession: GSE130038 dataset_title: Elevated colonic mucin expression correlates with extended time to surgery for ulcerative colitis patients organism: Homo sapiens ass... controlled vocabulary controlled vocabulary tissue match: colon

tissue intestine GSE130038 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence intestinal dataset_accession: GSE130038 dataset_title: Elevated colonic mucin expression correlates with extended time to surgery for ulcerative colitis patients organism: Homo sapiens ass... controlled vocabulary controlled vocabulary tissue match: intestinal

tissue colon GSM3730677 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon G155-01 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Male; smoking history: ex smoker; age at diagnosis: 34.86; age at surgery: 37.00; bmi: 25.30 controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM3730678 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon G155-02 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Female; smoking history: Never Smoked; age at diagnosis: 43.76; age at surgery: 54.96; bmi: 34.10 controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM3730679 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon G155-03 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Male; smoking history: Never Smoked; age at diagnosis: 77.52; age at surgery: 80.00; bmi: 25.80 controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM3730680 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon G155-04 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Male; smoking history: ex smoker; age at diagnosis: 54.89; age at surgery: 56.86; bmi: 26.10 controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM3730681 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon G155-05 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Female; smoking history: ex smoker; age at diagnosis: 64.58; age at surgery: 67.00; bmi: 22.90 controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM3730682 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon G155-06 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Female; smoking history: ex smoker; age at diagnosis: 47.55; age at surgery: 57.00; bmi: 20.40 controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM3730683 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon G155-07 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Female; smoking history: ex smoker; age at diagnosis: 50.80; age at surgery: 75.47; bmi: 28.12 controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM3730684 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon G155-08 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Male; smoking history: ex smoker; age at diagnosis: 26.50; age at surgery: 32.13; bmi: 26.85 controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM3730685 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon G155-09 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Female; smoking history: ex smoker; age at diagnosis: 65.01; age at surgery: 66.62; bmi: 30.00 controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM3730686 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon G155-10 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Female; smoking history: ex smoker; age at diagnosis: 48.02; age at surgery: 54.34; bmi: 27.00 controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM3730687 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon G155-11 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Female; smoking history: Never Smoked; age at diagnosis: 31.89; age at surgery: 33.55; bmi: 22.30 controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM3730688 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon G155-12 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Female; smoking history: ex smoker; age at diagnosis: 29.73; age at surgery: 45.00; bmi: 26.99 controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM3730689 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon G155-13 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Male; smoking history: ex smoker; age at diagnosis: 30.39; age at surgery: 40.15; bmi: 35.80 controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM3730690 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon G155-14 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Female; smoking history: Never Smoked; age at diagnosis: 33.30; age at surgery: 36.00; bmi: 37.37 controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM3730691 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon G155-15 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Female; smoking history: Never Smoked; age at diagnosis: 28.97; age at surgery: 36.71; bmi: 21.08 controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM3730692 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon G155-16 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Male; smoking history: ex smoker; age at diagnosis: 71.80; age at surgery: 73.93; bmi: 28.23 controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM3730693 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon G155-17 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Male; smoking history: Never Smoked; age at diagnosis: 55.61; age at surgery: 59.63; bmi: 28.87 controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM3730694 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon G155-18 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Male; smoking history: ex smoker; age at diagnosis: 61.86; age at surgery: 64.13; bmi: 19.80 controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM3730695 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon G155-19 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Male; smoking history: Never Smoked; age at diagnosis: 38.69; age at surgery: 40.00; bmi: 24.91 controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM3730696 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon G155-20 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Male; smoking history: ex smoker; age at diagnosis: 51.58; age at surgery: 53.58; bmi: 26.87 controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM3730697 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon G155-22 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Male; smoking history: Never Smoked; age at diagnosis: 39.82; age at surgery: 45.46; bmi: 31.06 controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM3730698 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon G155-23 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Female; smoking history: Never Smoked; age at diagnosis: 28.87; age at surgery: 41.57; bmi: 21.39 controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM3730699 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon G155-24 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Female; smoking history: ex smoker; age at diagnosis: 20.85; age at surgery: 37.00; bmi: 20.00 controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM3730700 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon G155-25 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Male; smoking history: ex smoker; age at diagnosis: 37.01; age at surgery: 43.20; bmi: 25.80 controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM3730701 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon G155-26 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Male; smoking history: Never Smoked; age at diagnosis: 27.76; age at surgery: 48.74; bmi: 34.01 controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM3730702 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon G155-27 sigmoid colon tissue disease: UC; tissue: sigmoid colon; Sex: Male; smoking history: ex smoker; age at diagnosis: 72.66; age at surgery: 75.01; bmi: 22.07 controlled vocabulary controlled vocabulary tissue match: colon

Sample Group Preview

26 rows shown Show Hide

Study totals: Case 26 | Control 0 | Unassigned 0 | Excluded 0 | Ambiguous 0 26 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Ulcerative colitis	Case	GSM3730677	G155-01	Sigmoid colon tissue Disease: UC; Tissue: Sigmoid colon; Sex: Male; Smoking history: Ex smoker; Age at diagnosis: 34.86; Age at surgery: 37.00; Bmi: 25.30	Case marker detected.
Ulcerative colitis	Case	GSM3730678	G155-02	Sigmoid colon tissue Disease: UC; Tissue: Sigmoid colon; Sex: Female; Smoking history: Never Smoked; Age at diagnosis: 43.76; Age at surgery: 54.96; Bmi: 34.10	Case marker detected.
Ulcerative colitis	Case	GSM3730679	G155-03	Sigmoid colon tissue Disease: UC; Tissue: Sigmoid colon; Sex: Male; Smoking history: Never Smoked; Age at diagnosis: 77.52; Age at surgery: 80.00; Bmi: 25.80	Case marker detected.
Ulcerative colitis	Case	GSM3730680	G155-04	Sigmoid colon tissue Disease: UC; Tissue: Sigmoid colon; Sex: Male; Smoking history: Ex smoker; Age at diagnosis: 54.89; Age at surgery: 56.86; Bmi: 26.10	Case marker detected.
Ulcerative colitis	Case	GSM3730681	G155-05	Sigmoid colon tissue Disease: UC; Tissue: Sigmoid colon; Sex: Female; Smoking history: Ex smoker; Age at diagnosis: 64.58; Age at surgery: 67.00; Bmi: 22.90	Case marker detected.
Ulcerative colitis	Case	GSM3730682	G155-06	Sigmoid colon tissue Disease: UC; Tissue: Sigmoid colon; Sex: Female; Smoking history: Ex smoker; Age at diagnosis: 47.55; Age at surgery: 57.00; Bmi: 20.40	Case marker detected.
Ulcerative colitis	Case	GSM3730683	G155-07	Sigmoid colon tissue Disease: UC; Tissue: Sigmoid colon; Sex: Female; Smoking history: Ex smoker; Age at diagnosis: 50.80; Age at surgery: 75.47; Bmi: 28.12	Case marker detected.
Ulcerative colitis	Case	GSM3730684	G155-08	Sigmoid colon tissue Disease: UC; Tissue: Sigmoid colon; Sex: Male; Smoking history: Ex smoker; Age at diagnosis: 26.50; Age at surgery: 32.13; Bmi: 26.85	Case marker detected.
Ulcerative colitis	Case	GSM3730685	G155-09	Sigmoid colon tissue Disease: UC; Tissue: Sigmoid colon; Sex: Female; Smoking history: Ex smoker; Age at diagnosis: 65.01; Age at surgery: 66.62; Bmi: 30.00	Case marker detected.
Ulcerative colitis	Case	GSM3730686	G155-10	Sigmoid colon tissue Disease: UC; Tissue: Sigmoid colon; Sex: Female; Smoking history: Ex smoker; Age at diagnosis: 48.02; Age at surgery: 54.34; Bmi: 27.00	Case marker detected.
Ulcerative colitis	Case	GSM3730687	G155-11	Sigmoid colon tissue Disease: UC; Tissue: Sigmoid colon; Sex: Female; Smoking history: Never Smoked; Age at diagnosis: 31.89; Age at surgery: 33.55; Bmi: 22.30	Case marker detected.
Ulcerative colitis	Case	GSM3730688	G155-12	Sigmoid colon tissue Disease: UC; Tissue: Sigmoid colon; Sex: Female; Smoking history: Ex smoker; Age at diagnosis: 29.73; Age at surgery: 45.00; Bmi: 26.99	Case marker detected.
Ulcerative colitis	Case	GSM3730689	G155-13	Sigmoid colon tissue Disease: UC; Tissue: Sigmoid colon; Sex: Male; Smoking history: Ex smoker; Age at diagnosis: 30.39; Age at surgery: 40.15; Bmi: 35.80	Case marker detected.
Ulcerative colitis	Case	GSM3730690	G155-14	Sigmoid colon tissue Disease: UC; Tissue: Sigmoid colon; Sex: Female; Smoking history: Never Smoked; Age at diagnosis: 33.30; Age at surgery: 36.00; Bmi: 37.37	Case marker detected.
Ulcerative colitis	Case	GSM3730691	G155-15	Sigmoid colon tissue Disease: UC; Tissue: Sigmoid colon; Sex: Female; Smoking history: Never Smoked; Age at diagnosis: 28.97; Age at surgery: 36.71; Bmi: 21.08	Case marker detected.
Ulcerative colitis	Case	GSM3730692	G155-16	Sigmoid colon tissue Disease: UC; Tissue: Sigmoid colon; Sex: Male; Smoking history: Ex smoker; Age at diagnosis: 71.80; Age at surgery: 73.93; Bmi: 28.23	Case marker detected.
Ulcerative colitis	Case	GSM3730693	G155-17	Sigmoid colon tissue Disease: UC; Tissue: Sigmoid colon; Sex: Male; Smoking history: Never Smoked; Age at diagnosis: 55.61; Age at surgery: 59.63; Bmi: 28.87	Case marker detected.
Ulcerative colitis	Case	GSM3730694	G155-18	Sigmoid colon tissue Disease: UC; Tissue: Sigmoid colon; Sex: Male; Smoking history: Ex smoker; Age at diagnosis: 61.86; Age at surgery: 64.13; Bmi: 19.80	Case marker detected.
Ulcerative colitis	Case	GSM3730695	G155-19	Sigmoid colon tissue Disease: UC; Tissue: Sigmoid colon; Sex: Male; Smoking history: Never Smoked; Age at diagnosis: 38.69; Age at surgery: 40.00; Bmi: 24.91	Case marker detected.
Ulcerative colitis	Case	GSM3730696	G155-20	Sigmoid colon tissue Disease: UC; Tissue: Sigmoid colon; Sex: Male; Smoking history: Ex smoker; Age at diagnosis: 51.58; Age at surgery: 53.58; Bmi: 26.87	Case marker detected.
Ulcerative colitis	Case	GSM3730697	G155-22	Sigmoid colon tissue Disease: UC; Tissue: Sigmoid colon; Sex: Male; Smoking history: Never Smoked; Age at diagnosis: 39.82; Age at surgery: 45.46; Bmi: 31.06	Case marker detected.
Ulcerative colitis	Case	GSM3730698	G155-23	Sigmoid colon tissue Disease: UC; Tissue: Sigmoid colon; Sex: Female; Smoking history: Never Smoked; Age at diagnosis: 28.87; Age at surgery: 41.57; Bmi: 21.39	Case marker detected.
Ulcerative colitis	Case	GSM3730699	G155-24	Sigmoid colon tissue Disease: UC; Tissue: Sigmoid colon; Sex: Female; Smoking history: Ex smoker; Age at diagnosis: 20.85; Age at surgery: 37.00; Bmi: 20.00	Case marker detected.
Ulcerative colitis	Case	GSM3730700	G155-25	Sigmoid colon tissue Disease: UC; Tissue: Sigmoid colon; Sex: Male; Smoking history: Ex smoker; Age at diagnosis: 37.01; Age at surgery: 43.20; Bmi: 25.80	Case marker detected.
Ulcerative colitis	Case	GSM3730701	G155-26	Sigmoid colon tissue Disease: UC; Tissue: Sigmoid colon; Sex: Male; Smoking history: Never Smoked; Age at diagnosis: 27.76; Age at surgery: 48.74; Bmi: 34.01	Case marker detected.
Ulcerative colitis	Case	GSM3730702	G155-27	Sigmoid colon tissue Disease: UC; Tissue: Sigmoid colon; Sex: Male; Smoking history: Ex smoker; Age at diagnosis: 72.66; Age at surgery: 75.01; Bmi: 22.07	Case marker detected.

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External Validation Finder

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

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Use as Discovery Cohort