Pouch transcriptional differences between UC and FAP indicate altered immune response.

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

16 case / 20 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: 36 samples
Specimen: Tissue
Reported/interpreted study design: Disease/model vs control Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Paziewska A, Horbacka K, Goryca K, Mikula M, Jarosz D, Dabrowska M, Krokowicz P, Karon J, Ostrowski J
Contact name: Krzysztof Goryca
Submission date: 2013-09-11
Last update: 2018-08-13
Organization: Uniwersytet Warszawski
Department: CeNT
Public date: 2014-05-01
Experiment types: Expression profiling by array
Platforms: GPL10558 Illumina HumanHT-12 V4.0 expression beadchip
Series type: Series
SubSeries: Not available
BioProject: PRJNA218882

Summary

A total proctocolectomy with ileal pouch-anal anastomosis (IPAA) is considered the surgery of choice for definitive management of familial adenomatous polyposis (FAP) and selected patients with ulcerative colitis (UC). However, this surgical treatment often associates with a long-term complication, pouchitis, which occurs mostly in UC patients. To better define the molecular background of pouchitis, the microarray-based survey was performed using pouch mucosal samples collected from 28 and 8 patients operated for UC and FAP, respectively. A number of 4771 genes was significantly differentiating uninflamed from inflamed mucosal samples, and their functional features were represented mostly by alerted metabolic and cell proliferation pathways. In contrast, functional analyses of aberrantly expressed probe sets between UC and FAP samples, irrespectively of mucosal inflammation status, revealed multiple pathways and terms which were linked to changes in immune response. Noteworthy, the comparison of uninflamed UC and FAP samples distinguished a set of 26 altered mRNAs including inflammation-related transcript encoding a Charcot-Leyden crystal (CLC) protein. The most discrete changes in gene expression profiles differentiating uninflamed UC and FAP mucosal samples were attributed to a Gene Ontology category innate immune response. Our study confirmed alterations of the immune responses as dominant in UC pouchitis which were earlier found in the studies using analyses of singular molecular elements. This observation may be important when managing IPAA patients.

Overall design

Each sample represents three biopsies taken from single patient, from the same areas of the lower part of the pouch mucosa (above the rectal cuff) during endoscopic examination. 28 patients underwent surgery for UC and 8 patients for FAP.

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 36 GSM samples	Primary source
recount3	Planned trusted source for processed count availability.	No match found
Expression Atlas	Planned source for curated expression experiment links.	No match found
PubMed	Publication context when PubMed identifiers are already known.	No match found

Metadata Quality Components

Persisted metadata quality

100 pts

Clarity: 100%
Weight: 100 pts

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

Analysis Readiness

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 Ulcerative colitis Disease context came from Normalization rules.
Likely case group Inflamed tissue 16 samples
Likely control group Non-inflamed tissue 20 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: Ulcerative colitis.
Processed data is available for downstream review.

Cautions

Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
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.
Multiple disease or phenotype arms were detected. The displayed grouping summarizes the full dataset; select the requested disease-specific contrast before analysis.
Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.

Normalized Fields

69 fields

Field Value Source Derived by Confidence Evidence Reason

assay_type microarray GSE50788 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence microarray dataset_accession: GSE50788 dataset_title: Pouch transcriptional differences between UC and FAP indicate altered immune response. organism: Homo sapiens assay_type: microarray p... keyword match keyword match: microarray

disease ulcerative colitis GSE50788 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis dataset_accession: GSE50788 dataset_title: Pouch transcriptional differences between UC and FAP indicate altered immune response. organism: Homo sapiens assay_type: microarray p... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1229209 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis 3 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: uninflamed controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1229210 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis 8 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: uninflamed controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1229211 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis 12 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: uninflamed controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1229212 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis 15 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: uninflamed controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1229213 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis 16 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: uninflamed controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1229214 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis 18 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: uninflamed controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1229215 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis 25 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: uninflamed controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1229216 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis 21 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: uninflamed controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1229217 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis 31 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: uninflamed controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1229218 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis 36 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: uninflamed controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1229219 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis 23 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: uninflamed controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1229220 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis 40 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: inflamed controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1229221 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis 4 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: inflamed controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1229222 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis 5 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: inflamed controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1229223 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis 10 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: inflamed controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1229224 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis 11 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: inflamed controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1229225 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis 17 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: inflamed controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1229226 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis 38 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: uninflamed controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1229227 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis 32 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: uninflamed controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1229228 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis 35 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: uninflamed controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1229229 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis 43 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: uninflamed controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1229230 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis 26 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: inflamed controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1229231 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis 29 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: inflamed controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1229232 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis 41 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: inflamed controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1229233 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis 42 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: inflamed controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1229234 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis 49 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: inflamed controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1229235 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis 24 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: inflamed controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1229236 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis 7 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: inflamed controlled vocabulary controlled vocabulary disease match: ulcerative colitis

organism Homo sapiens GSE50788 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE50788 dataset_title: Pouch transcriptional differences between UC and FAP indicate altered immune response. organism: Homo sapiens assay_type: microarray p... keyword match keyword match: homo sapiens

sample_type non-inflamed tissue GSM1229209 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence uninflamed 3 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: uninflamed controlled vocabulary controlled vocabulary sample type match: uninflamed

sample_type non-inflamed tissue GSM1229210 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence uninflamed 8 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: uninflamed controlled vocabulary controlled vocabulary sample type match: uninflamed

sample_type non-inflamed tissue GSM1229211 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence uninflamed 12 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: uninflamed controlled vocabulary controlled vocabulary sample type match: uninflamed

sample_type non-inflamed tissue GSM1229212 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence uninflamed 15 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: uninflamed controlled vocabulary controlled vocabulary sample type match: uninflamed

sample_type non-inflamed tissue GSM1229213 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence uninflamed 16 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: uninflamed controlled vocabulary controlled vocabulary sample type match: uninflamed

sample_type non-inflamed tissue GSM1229214 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence uninflamed 18 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: uninflamed controlled vocabulary controlled vocabulary sample type match: uninflamed

sample_type non-inflamed tissue GSM1229215 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence uninflamed 25 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: uninflamed controlled vocabulary controlled vocabulary sample type match: uninflamed

sample_type non-inflamed tissue GSM1229216 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence uninflamed 21 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: uninflamed controlled vocabulary controlled vocabulary sample type match: uninflamed

sample_type non-inflamed tissue GSM1229217 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence uninflamed 31 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: uninflamed controlled vocabulary controlled vocabulary sample type match: uninflamed

sample_type non-inflamed tissue GSM1229218 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence uninflamed 36 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: uninflamed controlled vocabulary controlled vocabulary sample type match: uninflamed

sample_type non-inflamed tissue GSM1229219 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence uninflamed 23 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: uninflamed controlled vocabulary controlled vocabulary sample type match: uninflamed

sample_type inflamed tissue GSM1229220 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed 40 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: inflamed controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type inflamed tissue GSM1229221 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed 4 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: inflamed controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type inflamed tissue GSM1229222 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed 5 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: inflamed controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type inflamed tissue GSM1229223 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed 10 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: inflamed controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type inflamed tissue GSM1229224 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed 11 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: inflamed controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type inflamed tissue GSM1229225 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed 17 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: inflamed controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type non-inflamed tissue GSM1229226 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence uninflamed 38 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: uninflamed controlled vocabulary controlled vocabulary sample type match: uninflamed

sample_type non-inflamed tissue GSM1229227 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence uninflamed 32 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: uninflamed controlled vocabulary controlled vocabulary sample type match: uninflamed

sample_type non-inflamed tissue GSM1229228 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence uninflamed 35 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: uninflamed controlled vocabulary controlled vocabulary sample type match: uninflamed

sample_type non-inflamed tissue GSM1229229 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence uninflamed 43 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: uninflamed controlled vocabulary controlled vocabulary sample type match: uninflamed

sample_type inflamed tissue GSM1229230 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed 26 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: inflamed controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type inflamed tissue GSM1229231 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed 29 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: inflamed controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type inflamed tissue GSM1229232 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed 41 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: inflamed controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type inflamed tissue GSM1229233 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed 42 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: inflamed controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type inflamed tissue GSM1229234 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed 49 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: inflamed controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type inflamed tissue GSM1229235 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed 24 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: inflamed controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type inflamed tissue GSM1229236 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed 7 UC_pouch mucosa condition: ulcerative colitis (UC); inflammation status: inflamed controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type non-inflamed tissue GSM1229237 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence uninflamed 13 FAP_pouch mucosa condition: familial adenomatous polyposis (FAP); inflammation status: uninflamed controlled vocabulary controlled vocabulary sample type match: uninflamed

sample_type non-inflamed tissue GSM1229238 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence uninflamed 14 FAP_pouch mucosa condition: familial adenomatous polyposis (FAP); inflammation status: uninflamed controlled vocabulary controlled vocabulary sample type match: uninflamed

sample_type inflamed tissue GSM1229239 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed 19 FAP_pouch mucosa condition: familial adenomatous polyposis (FAP); inflammation status: inflamed controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type non-inflamed tissue GSM1229240 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence uninflamed 22 FAP_pouch mucosa condition: familial adenomatous polyposis (FAP); inflammation status: uninflamed controlled vocabulary controlled vocabulary sample type match: uninflamed

sample_type non-inflamed tissue GSM1229241 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence uninflamed 37 FAP_pouch mucosa condition: familial adenomatous polyposis (FAP); inflammation status: uninflamed controlled vocabulary controlled vocabulary sample type match: uninflamed

sample_type non-inflamed tissue GSM1229242 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence uninflamed 44 FAP_pouch mucosa condition: familial adenomatous polyposis (FAP); inflammation status: uninflamed controlled vocabulary controlled vocabulary sample type match: uninflamed

sample_type inflamed tissue GSM1229243 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed 45 FAP_pouch mucosa condition: familial adenomatous polyposis (FAP); inflammation status: inflamed controlled vocabulary controlled vocabulary sample type match: inflamed

sample_type inflamed tissue GSM1229244 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence inflamed 46 FAP_pouch mucosa condition: familial adenomatous polyposis (FAP); inflammation status: inflamed controlled vocabulary controlled vocabulary sample type match: inflamed

tissue colon GSE50788 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence rectal dataset_accession: GSE50788 dataset_title: Pouch transcriptional differences between UC and FAP indicate altered immune response. organism: Homo sapiens assay_type: microarray p... controlled vocabulary controlled vocabulary tissue match: rectal

tissue intestine GSE50788 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ileal dataset_accession: GSE50788 dataset_title: Pouch transcriptional differences between UC and FAP indicate altered immune response. organism: Homo sapiens assay_type: microarray p... controlled vocabulary controlled vocabulary tissue match: ileal

Sample Group Preview

36 rows shown Show Hide

Study totals: Case 16 | Control 20 | Unassigned 0 | Excluded 0 | Ambiguous 0 36 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Inflamed tissue	Case	GSM1229220	40	UC_pouch mucosa Condition: Ulcerative colitis (UC); Inflammation status: Inflamed	Case marker detected.
Inflamed tissue	Case	GSM1229221	4	UC_pouch mucosa Condition: Ulcerative colitis (UC); Inflammation status: Inflamed	Case marker detected.
Inflamed tissue	Case	GSM1229222	5	UC_pouch mucosa Condition: Ulcerative colitis (UC); Inflammation status: Inflamed	Case marker detected.
Inflamed tissue	Case	GSM1229223	10	UC_pouch mucosa Condition: Ulcerative colitis (UC); Inflammation status: Inflamed	Case marker detected.
Inflamed tissue	Case	GSM1229224	11	UC_pouch mucosa Condition: Ulcerative colitis (UC); Inflammation status: Inflamed	Case marker detected.
Inflamed tissue	Case	GSM1229225	17	UC_pouch mucosa Condition: Ulcerative colitis (UC); Inflammation status: Inflamed	Case marker detected.
Inflamed tissue	Case	GSM1229230	26	UC_pouch mucosa Condition: Ulcerative colitis (UC); Inflammation status: Inflamed	Case marker detected.
Inflamed tissue	Case	GSM1229231	29	UC_pouch mucosa Condition: Ulcerative colitis (UC); Inflammation status: Inflamed	Case marker detected.
Inflamed tissue	Case	GSM1229232	41	UC_pouch mucosa Condition: Ulcerative colitis (UC); Inflammation status: Inflamed	Case marker detected.
Inflamed tissue	Case	GSM1229233	42	UC_pouch mucosa Condition: Ulcerative colitis (UC); Inflammation status: Inflamed	Case marker detected.
Inflamed tissue	Case	GSM1229234	49	UC_pouch mucosa Condition: Ulcerative colitis (UC); Inflammation status: Inflamed	Case marker detected.
Inflamed tissue	Case	GSM1229235	24	UC_pouch mucosa Condition: Ulcerative colitis (UC); Inflammation status: Inflamed	Case marker detected.
Inflamed tissue	Case	GSM1229236	7	UC_pouch mucosa Condition: Ulcerative colitis (UC); Inflammation status: Inflamed	Case marker detected.
Inflamed tissue	Case	GSM1229239	19	FAP_pouch mucosa Condition: Familial adenomatous polyposis (FAP); Inflammation status: Inflamed	Case marker detected.
Inflamed tissue	Case	GSM1229243	45	FAP_pouch mucosa Condition: Familial adenomatous polyposis (FAP); Inflammation status: Inflamed	Case marker detected.
Inflamed tissue	Case	GSM1229244	46	FAP_pouch mucosa Condition: Familial adenomatous polyposis (FAP); Inflammation status: Inflamed	Case marker detected.
Non-inflamed tissue	Control	GSM1229209	3	UC_pouch mucosa Condition: Ulcerative colitis (UC); Inflammation status: Uninflamed	Control marker detected.
Non-inflamed tissue	Control	GSM1229210	8	UC_pouch mucosa Condition: Ulcerative colitis (UC); Inflammation status: Uninflamed	Control marker detected.
Non-inflamed tissue	Control	GSM1229211	12	UC_pouch mucosa Condition: Ulcerative colitis (UC); Inflammation status: Uninflamed	Control marker detected.
Non-inflamed tissue	Control	GSM1229212	15	UC_pouch mucosa Condition: Ulcerative colitis (UC); Inflammation status: Uninflamed	Control marker detected.
Non-inflamed tissue	Control	GSM1229213	16	UC_pouch mucosa Condition: Ulcerative colitis (UC); Inflammation status: Uninflamed	Control marker detected.
Non-inflamed tissue	Control	GSM1229214	18	UC_pouch mucosa Condition: Ulcerative colitis (UC); Inflammation status: Uninflamed	Control marker detected.
Non-inflamed tissue	Control	GSM1229215	25	UC_pouch mucosa Condition: Ulcerative colitis (UC); Inflammation status: Uninflamed	Control marker detected.
Non-inflamed tissue	Control	GSM1229216	21	UC_pouch mucosa Condition: Ulcerative colitis (UC); Inflammation status: Uninflamed	Control marker detected.
Non-inflamed tissue	Control	GSM1229217	31	UC_pouch mucosa Condition: Ulcerative colitis (UC); Inflammation status: Uninflamed	Control marker detected.
Non-inflamed tissue	Control	GSM1229218	36	UC_pouch mucosa Condition: Ulcerative colitis (UC); Inflammation status: Uninflamed	Control marker detected.
Non-inflamed tissue	Control	GSM1229219	23	UC_pouch mucosa Condition: Ulcerative colitis (UC); Inflammation status: Uninflamed	Control marker detected.
Non-inflamed tissue	Control	GSM1229226	38	UC_pouch mucosa Condition: Ulcerative colitis (UC); Inflammation status: Uninflamed	Control marker detected.
Non-inflamed tissue	Control	GSM1229227	32	UC_pouch mucosa Condition: Ulcerative colitis (UC); Inflammation status: Uninflamed	Control marker detected.
Non-inflamed tissue	Control	GSM1229228	35	UC_pouch mucosa Condition: Ulcerative colitis (UC); Inflammation status: Uninflamed	Control marker detected.
Non-inflamed tissue	Control	GSM1229229	43	UC_pouch mucosa Condition: Ulcerative colitis (UC); Inflammation status: Uninflamed	Control marker detected.
Non-inflamed tissue	Control	GSM1229237	13	FAP_pouch mucosa Condition: Familial adenomatous polyposis (FAP); Inflammation status: Uninflamed	Control marker detected.
Non-inflamed tissue	Control	GSM1229238	14	FAP_pouch mucosa Condition: Familial adenomatous polyposis (FAP); Inflammation status: Uninflamed	Control marker detected.
Non-inflamed tissue	Control	GSM1229240	22	FAP_pouch mucosa Condition: Familial adenomatous polyposis (FAP); Inflammation status: Uninflamed	Control marker detected.
Non-inflamed tissue	Control	GSM1229241	37	FAP_pouch mucosa Condition: Familial adenomatous polyposis (FAP); Inflammation status: Uninflamed	Control marker detected.
Non-inflamed tissue	Control	GSM1229242	44	FAP_pouch mucosa Condition: Familial adenomatous polyposis (FAP); Inflammation status: Uninflamed	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.