GSE22619

Genome wide expression data from discordant twins (ulcerative colitis, primary mucosal tissue)

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

10 case / 2 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: Häsler R, Haesler R
Contact name: Robert Haesler
Submission date: 2010-06-29
Last update: 2019-03-25
Organization: University Clinic of Schleswig Holstein
Department: IKMB / 1st Dept. of Medicine
Public date: 2012-01-18
Experiment types: Expression profiling by array
Platforms: GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
Series type: Series
SubSeries: Not available
BioProject: PRJNA128513

Summary

Background and aims. The etiopathology of inflammatory bowel diseases is still poorly understood. To date, only few little data are available on the microbiota composition in ulcerative colitis (UC), representing a major subform of inflammatory bowel diseases. Currently, one of the main challenges is to unravel the interactions between genetics and environmental factors in the onset or during the progression and maintenance of the disease. The aim of the present study was to analyse twin pairs discordant for UC for both gut microbiota dysbiosis and host expression profiles at a mucosal level and to get insight into the functional genomic crosstalk between microbiota and mucosal epithelium in vivo. Methods. Biopsies were sampled from the sigmoid colon of both healthy and diseased siblings from UC discordant twin pairs but also from healthy twins. Microbiota profiles were assessed by 16S rDNA libraries while mRNA expression profiles were analysed from the same volunteers using Affymetrix microarrays. Results. UC patients showed a dysbiotic microbiota with lower diversity and more species belonging to Actinobacteria and Proteobacteria phyla. On the contrary, their healthy siblings’ microbiota contained more bacteria from the Lachnospiracea and Ruminococcaceae family than did healthy individuals . Sixty-three host transcripts significantly correlated with bacterial genera in healthy individuals whereas only 43 and 32 correlated with bacteria in healthy and UC siblings from discordant pairs, respectively. Several transcripts related to oxidative and immune responses were differentially expressed between unaffected and UC siblings. Conclusion. A loss of crosstalk between gut microbiota and host was highlighted in UC patients. This defect was also striking in healthy siblings from discordant pairs, as was the lower biodiversity within the microbiota. Our results suggest disease-relevant interactions between host transcriptome and microbiota. Moreover, unusual aerobic bacteria were noticed in UC mucosal microbiota, whereas healthy siblings from discordant pairs had higher percentages of potentially beneficialusual commensal bacterial species.

Overall design

Paired samples (twins) were analyzed to obtain data independent of genetic variation Samples GSM560961-GSM560976 correspond to publication with PMID: 21621540. Samples GSM560961-GSM560976, GSM1012177-GSM1012180 correspond to publication with PMID: 22826509.

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. 2 linked publications 2 DOIs Primary publication Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis. Gastroenterology, 2011 PubMed DOI A functional methylome map of ulcerative colitis. Genome research, 2012 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

Review before analysis

85% 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

3/15 pts

Unassigned or review-needed samples remain before analysis.

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

8 samples are still unassigned.

Next Steps

Resolve unassigned or review-needed samples in the grouping table.

Analysis Preparation Checklist

4/6 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

Needs review

0 review-needed samples and 8 unassigned samples remain.

Resolve ambiguous and unassigned samples before finalizing the contrast.

Exclusion decisions recorded

Ready

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

Record any manual exclusions in the downstream analysis notes.

Source traceability preserved

Ready

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

Keep GEO accessions with exported metadata.

Bioinformatician Review

Bioinformatician review required

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

Analysis readiness has blockers that must be resolved before DE.

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

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 Ulcerative colitis 10 samples
Likely control group Non-inflamed tissue 2 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.
External evidence: PubMed links 2 publications; 2 DOIs available: PMID 21621540, PMID 22826509.
Publication context: Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis.. Gastroenterology, 2011. PMID 21621540. DOI 10.1053/j.gastro.2011.04.011.
Publication context: A functional methylome map of ulcerative colitis.. Genome research, 2012. PMID 22826509. DOI 10.1101/gr.138347.112.

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

59 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source colon GSM1012177 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: primary mucosal tissue, colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1012178 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: primary mucosal tissue, colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1012179 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: primary mucosal tissue, colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1012180 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: primary mucosal tissue, colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM560961 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon, mucosal tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM560962 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon, mucosal tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM560963 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon, mucosal tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM560964 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon, mucosal tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM560965 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon, mucosal tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM560966 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon, mucosal tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM560967 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon, mucosal tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM560968 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon, mucosal tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM560969 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon, mucosal tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM560970 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon, mucosal tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM560971 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon, mucosal tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM560972 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon, mucosal tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM560973 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon, mucosal tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM560974 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon, mucosal tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM560975 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon, mucosal tissue sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM560976 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon, mucosal tissue sample-anatomical-source-v1 sample-local anatomical source

assay_type microarray GSE22619 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence microarray dataset_accession: GSE22619 dataset_title: Genome wide expression data from discordant twins (ulcerative colitis, primary mucosal tissue) organism: Homo sapiens assay_type: micr... keyword match keyword match: microarray

disease inflammatory bowel disease GSE22619 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflammatory bowel dataset_accession: GSE22619 dataset_title: Genome wide expression data from discordant twins (ulcerative colitis, primary mucosal tissue) organism: Homo sapiens assay_type: micr... controlled vocabulary controlled vocabulary disease match: inflammatory bowel

disease ulcerative colitis GSE22619 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis dataset_accession: GSE22619 dataset_title: Genome wide expression data from discordant twins (ulcerative colitis, primary mucosal tissue) organism: Homo sapiens assay_type: micr... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1012178 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Diseased individual (ulcerative colitis) of twinpair #2 primary mucosal tissue, colon twin pair: #2; individual: diseased individual, inflamed; tissue: primary mucosal tissue, c... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1012180 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Diseased individual (ulcerative colitis) of twinpair #3 primary mucosal tissue, colon twin pair: #3; individual: diseased individual, inflamed; tissue: primary mucosal tissue, c... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM560969 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Diseased individual (ulcerative colitis) of twinpair #1 primary mucosal tissue, colon twin pair: #1; individual: diseased; tissue: colon, mucosal tissue; mean age: 31.5 years old controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM560970 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Diseased individual (ulcerative colitis) of twinpair #4 primary mucosal tissue, colon twin pair: #4; individual: diseased; tissue: colon, mucosal tissue; mean age: 31.5 years old controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM560971 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Diseased individual (ulcerative colitis) of twinpair #6 primary mucosal tissue, colon twin pair: #6; individual: diseased; tissue: colon, mucosal tissue; mean age: 31.5 years old controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM560972 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Diseased individual (ulcerative colitis) of twinpair #7 primary mucosal tissue, colon twin pair: #7; individual: diseased; tissue: colon, mucosal tissue; mean age: 31.5 years old controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM560973 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Diseased individual (ulcerative colitis) of twinpair #8 primary mucosal tissue, colon twin pair: #8; individual: diseased; tissue: colon, mucosal tissue; mean age: 31.5 years old controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM560974 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Diseased individual (ulcerative colitis) of twinpair #9 primary mucosal tissue, colon twin pair: #9; individual: diseased; tissue: colon, mucosal tissue; mean age: 31.5 years old controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM560975 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Diseased individual (ulcerative colitis) of twinpair #10 primary mucosal tissue, colon twin pair: #10; individual: diseased; tissue: colon, mucosal tissue; mean age: 31.5 years old controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM560976 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Diseased individual (ulcerative colitis) of twinpair #12 primary mucosal tissue, colon twin pair: #12; individual: diseased; tissue: colon, mucosal tissue; mean age: 31.5 years old controlled vocabulary controlled vocabulary disease match: ulcerative colitis

organism Homo sapiens GSE22619 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE22619 dataset_title: Genome wide expression data from discordant twins (ulcerative colitis, primary mucosal tissue) organism: Homo sapiens assay_type: micr... keyword match keyword match: homo sapiens

sample_type non-inflamed tissue GSM1012177 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence non-inflamed Healthy individual of twinpair #2 primary mucosal tissue, colon twin pair: #2; individual: healthy individual, non-inflamed; tissue: primary mucosal tissue, colon; mean age: 31.5 controlled vocabulary controlled vocabulary sample type match: non-inflamed

sample_type inflamed tissue GSM1012178 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed Diseased individual (ulcerative colitis) of twinpair #2 primary mucosal tissue, colon twin pair: #2; individual: diseased individual, inflamed; tissue: primary mucosal tissue, c... controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type non-inflamed tissue GSM1012179 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence non-inflamed Healthy individual of twinpair #3 primary mucosal tissue, colon twin pair: #3; individual: healthy individual, non-inflamed; tissue: primary mucosal tissue, colon; mean age: 31.5 controlled vocabulary controlled vocabulary sample type match: non-inflamed

sample_type inflamed tissue GSM1012180 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed Diseased individual (ulcerative colitis) of twinpair #3 primary mucosal tissue, colon twin pair: #3; individual: diseased individual, inflamed; tissue: primary mucosal tissue, c... controlled vocabulary controlled vocabulary sample type match: inflamed

tissue colon GSE22619 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon dataset_accession: GSE22619 dataset_title: Genome wide expression data from discordant twins (ulcerative colitis, primary mucosal tissue) organism: Homo sapiens assay_type: micr... controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1012177 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Healthy individual of twinpair #2 primary mucosal tissue, colon twin pair: #2; individual: healthy individual, non-inflamed; tissue: primary mucosal tissue, colon; mean age: 31.5 controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1012178 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Diseased individual (ulcerative colitis) of twinpair #2 primary mucosal tissue, colon twin pair: #2; individual: diseased individual, inflamed; tissue: primary mucosal tissue, c... controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1012179 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Healthy individual of twinpair #3 primary mucosal tissue, colon twin pair: #3; individual: healthy individual, non-inflamed; tissue: primary mucosal tissue, colon; mean age: 31.5 controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1012180 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Diseased individual (ulcerative colitis) of twinpair #3 primary mucosal tissue, colon twin pair: #3; individual: diseased individual, inflamed; tissue: primary mucosal tissue, c... controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM560961 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Healthy individual of twinpair #1 primary mucosal tissue, colon twin pair: #1; individual: healthy; tissue: colon, mucosal tissue; mean age: 31.5 years old controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM560962 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Healthy individual of twinpair #4 primary mucosal tissue, colon twin pair: #4; individual: healthy; tissue: colon, mucosal tissue; mean age: 31.5 years old controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM560963 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Healthy individual of twinpair #6 primary mucosal tissue, colon twin pair: #6; individual: healthy; tissue: colon, mucosal tissue; mean age: 31.5 years old controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM560964 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Healthy individual of twinpair #7 primary mucosal tissue, colon twin pair: #7; individual: healthy; tissue: colon, mucosal tissue; mean age: 31.5 years old controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM560965 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Healthy individual of twinpair #8 primary mucosal tissue, colon twin pair: #8; individual: healthy; tissue: colon, mucosal tissue; mean age: 31.5 years old controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM560966 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Healthy individual of twinpair #9 primary mucosal tissue, colon twin pair: #9; individual: healthy; tissue: colon, mucosal tissue; mean age: 31.5 years old controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM560967 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Healthy individual of twinpair #10 primary mucosal tissue, colon twin pair: #10; individual: healthy; tissue: colon, mucosal tissue; mean age: 31.5 years old controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM560968 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Healthy individual of twinpair #12 primary mucosal tissue, colon twin pair: #12; individual: healthy; tissue: colon, mucosal tissue; mean age: 31.5 years old controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM560969 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Diseased individual (ulcerative colitis) of twinpair #1 primary mucosal tissue, colon twin pair: #1; individual: diseased; tissue: colon, mucosal tissue; mean age: 31.5 years old controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM560970 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Diseased individual (ulcerative colitis) of twinpair #4 primary mucosal tissue, colon twin pair: #4; individual: diseased; tissue: colon, mucosal tissue; mean age: 31.5 years old controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM560971 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Diseased individual (ulcerative colitis) of twinpair #6 primary mucosal tissue, colon twin pair: #6; individual: diseased; tissue: colon, mucosal tissue; mean age: 31.5 years old controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM560972 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Diseased individual (ulcerative colitis) of twinpair #7 primary mucosal tissue, colon twin pair: #7; individual: diseased; tissue: colon, mucosal tissue; mean age: 31.5 years old controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM560973 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Diseased individual (ulcerative colitis) of twinpair #8 primary mucosal tissue, colon twin pair: #8; individual: diseased; tissue: colon, mucosal tissue; mean age: 31.5 years old controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM560974 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Diseased individual (ulcerative colitis) of twinpair #9 primary mucosal tissue, colon twin pair: #9; individual: diseased; tissue: colon, mucosal tissue; mean age: 31.5 years old controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM560975 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Diseased individual (ulcerative colitis) of twinpair #10 primary mucosal tissue, colon twin pair: #10; individual: diseased; tissue: colon, mucosal tissue; mean age: 31.5 years old controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM560976 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Diseased individual (ulcerative colitis) of twinpair #12 primary mucosal tissue, colon twin pair: #12; individual: diseased; tissue: colon, mucosal tissue; mean age: 31.5 years old controlled vocabulary controlled vocabulary tissue match: colon

Sample Group Preview

20 rows shown Show Hide

Study totals: Case 10 | Control 2 | Unassigned 8 | Excluded 0 | Ambiguous 0 20 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Ulcerative colitis	Case	GSM560969	Diseased individual (ulcerative colitis) of twinpair #1	Primary mucosal tissue, colon Twin pair: #1; Individual: Diseased; Tissue: Colon, mucosal tissue; Mean age: 31.5 years old	Case marker detected.
Ulcerative colitis	Case	GSM560970	Diseased individual (ulcerative colitis) of twinpair #4	Primary mucosal tissue, colon Twin pair: #4; Individual: Diseased; Tissue: Colon, mucosal tissue; Mean age: 31.5 years old	Case marker detected.
Ulcerative colitis	Case	GSM560971	Diseased individual (ulcerative colitis) of twinpair #6	Primary mucosal tissue, colon Twin pair: #6; Individual: Diseased; Tissue: Colon, mucosal tissue; Mean age: 31.5 years old	Case marker detected.
Ulcerative colitis	Case	GSM560972	Diseased individual (ulcerative colitis) of twinpair #7	Primary mucosal tissue, colon Twin pair: #7; Individual: Diseased; Tissue: Colon, mucosal tissue; Mean age: 31.5 years old	Case marker detected.
Ulcerative colitis	Case	GSM560973	Diseased individual (ulcerative colitis) of twinpair #8	Primary mucosal tissue, colon Twin pair: #8; Individual: Diseased; Tissue: Colon, mucosal tissue; Mean age: 31.5 years old	Case marker detected.
Ulcerative colitis	Case	GSM560974	Diseased individual (ulcerative colitis) of twinpair #9	Primary mucosal tissue, colon Twin pair: #9; Individual: Diseased; Tissue: Colon, mucosal tissue; Mean age: 31.5 years old	Case marker detected.
Ulcerative colitis	Case	GSM560975	Diseased individual (ulcerative colitis) of twinpair #10	Primary mucosal tissue, colon Twin pair: #10; Individual: Diseased; Tissue: Colon, mucosal tissue; Mean age: 31.5 years old	Case marker detected.
Ulcerative colitis	Case	GSM560976	Diseased individual (ulcerative colitis) of twinpair #12	Primary mucosal tissue, colon Twin pair: #12; Individual: Diseased; Tissue: Colon, mucosal tissue; Mean age: 31.5 years old	Case marker detected.
Inflamed tissue	Case	GSM1012178	Diseased individual (ulcerative colitis) of twinpair #2	Primary mucosal tissue, colon Twin pair: #2; Individual: Diseased individual, inflamed; Tissue: Primary mucosal tissue, colon; Mean age: 31.5	Case marker detected.
Inflamed tissue	Case	GSM1012180	Diseased individual (ulcerative colitis) of twinpair #3	Primary mucosal tissue, colon Twin pair: #3; Individual: Diseased individual, inflamed; Tissue: Primary mucosal tissue, colon; Mean age: 31.5	Case marker detected.
Non-inflamed tissue	Control	GSM1012177	Healthy individual of twinpair #2	Primary mucosal tissue, colon Twin pair: #2; Individual: Healthy individual, non-inflamed; Tissue: Primary mucosal tissue, colon; Mean age: 31.5	Control marker detected.
Non-inflamed tissue	Control	GSM1012179	Healthy individual of twinpair #3	Primary mucosal tissue, colon Twin pair: #3; Individual: Healthy individual, non-inflamed; Tissue: Primary mucosal tissue, colon; Mean age: 31.5	Control marker detected.
Unassigned	Unassigned	GSM560961	Healthy individual of twinpair #1	Primary mucosal tissue, colon Twin pair: #1; Individual: Healthy; Tissue: Colon, mucosal tissue; Mean age: 31.5 years old	No explicit case or control marker detected.
Unassigned	Unassigned	GSM560962	Healthy individual of twinpair #4	Primary mucosal tissue, colon Twin pair: #4; Individual: Healthy; Tissue: Colon, mucosal tissue; Mean age: 31.5 years old	No explicit case or control marker detected.
Unassigned	Unassigned	GSM560963	Healthy individual of twinpair #6	Primary mucosal tissue, colon Twin pair: #6; Individual: Healthy; Tissue: Colon, mucosal tissue; Mean age: 31.5 years old	No explicit case or control marker detected.
Unassigned	Unassigned	GSM560964	Healthy individual of twinpair #7	Primary mucosal tissue, colon Twin pair: #7; Individual: Healthy; Tissue: Colon, mucosal tissue; Mean age: 31.5 years old	No explicit case or control marker detected.
Unassigned	Unassigned	GSM560965	Healthy individual of twinpair #8	Primary mucosal tissue, colon Twin pair: #8; Individual: Healthy; Tissue: Colon, mucosal tissue; Mean age: 31.5 years old	No explicit case or control marker detected.
Unassigned	Unassigned	GSM560966	Healthy individual of twinpair #9	Primary mucosal tissue, colon Twin pair: #9; Individual: Healthy; Tissue: Colon, mucosal tissue; Mean age: 31.5 years old	No explicit case or control marker detected.
Unassigned	Unassigned	GSM560967	Healthy individual of twinpair #10	Primary mucosal tissue, colon Twin pair: #10; Individual: Healthy; Tissue: Colon, mucosal tissue; Mean age: 31.5 years old	No explicit case or control marker detected.
Unassigned	Unassigned	GSM560968	Healthy individual of twinpair #12	Primary mucosal tissue, colon Twin pair: #12; Individual: Healthy; Tissue: Colon, mucosal tissue; Mean age: 31.5 years old	No explicit case or control marker detected.

Use as Discovery Cohort

External Validation Finder

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

Summary

Overall design

Source Evidence

Primary publication

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