GSE25277

Gene expression patterns of biopsies from a colonoscopy taken in 2009 of an ulcerative colitis patient infected with Trichuris trichiura

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

12 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: microarray
Organism: Homo sapiens
Whole-study samples: 12 samples
Specimen: Biopsy
Reported/interpreted study design: Unclear study design Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Broadhurst MJ, Leung JM, Kashyap V, McCune JM, Mahadevan U, McKerrow JH, Loke P, Batra S
Contact name: Sajeev Batra
Submission date: 2010-11-10
Last update: 2012-03-23
Organization: UCSF
Department: IRIBHM
Public date: 2010-11-20
Experiment types: Expression profiling by array
Platforms: GPL5621 SFGF HEEBO Human Set v1.00
Series type: SubSeries
SubSeries: Not available
BioProject: PRJNA142581

Summary

Helminth infection may have the potential to suppress intestinal inflammation in inflammatory bowel diseases. Ulcerative colitis is more common in developed countries than in developing countries endemic for helminth infections. There are animal models, as well as clinical trials, suggesting therapeutic effects of experimental helminth infection. Here, we provide a comprehensive molecular portrait of dynamic changes in the intestinal mucosa of an individual who infected himself with Trichuris trichiura to treat his symptoms of ulcerative colitis. Genes involved in carbohydrate and lipid metabolism were upregulated in helminth-colonized tissue, while tissues with active colitis showed upregulation of proinflammatory genes such as IL-17, IL13RA2, and CHI3L1. T. trichiura colonization of the intestine may reduce symptomatic colitis by promoting goblet cell hyperplasia and mucus production through TH2 cytokines and IL-22. By better understanding the physiological effects of helminth infection, new therapies for ulcerative colitis could be identified. This is the third (out of three) series of arrays from this patient from a colonoscopy in 2009 when the patient was in remission.

Overall design

We analyzed 12 HEEBO arrays on which were hybridized RNA amplified from pinch biopsies collected from different regions of the colon. 4 samples were from the ascending colon, which was colonized by worms at the time. 3 samples were from the transverse colon, which appeared normal at the time. 3 samples were from the recto-sigmoid colon, which had recovered from colitis at the time. 2 samples were from the terminal ileum, which was unaffected by worms or colitis.

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 12 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 IL-22+ CD4+ T cells are associated with therapeutic trichuris trichiura infection in an ulcerative colitis patient. Science translational medicine, 2010 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.

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

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

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 12 samples
Likely control group No control group detected 0 samples

Intent Interpretation

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

Ranking Facts

Supporting evidence

Interpreted disease metadata: Infectious disease or host response, Inflammatory bowel disease, Ulcerative colitis.
Processed data is available for downstream review.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 21123809.
Publication context: IL-22+ CD4+ T cells are associated with therapeutic trichuris trichiura infection in an ulcerative colitis patient.. Science translational medicine, 2010. PMID 21123809. DOI 10.1126/scitranslmed.3001500.

Cautions

Comparison: Unclear study design. Specimen: Biopsy. Comparison suitability: 0%.
Downgraded for tissue search because study design or specimen source is unclear.
Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
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 - Biopsy. 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.
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.
Patient-tissue tumor-normal intent requires clear tumor-normal grouping.

Normalized Fields

66 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source ileum GSM621958 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ileum tissue: terminal ileum biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source ileum GSM621959 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ileum tissue: terminal ileum biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM621960 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: ascending colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM621961 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: ascending colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM621962 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: ascending colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM621963 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: ascending colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM621964 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: transverse colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM621965 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: transverse colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM621966 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: transverse colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM621967 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM621968 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM621969 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: sigmoid colon biopsy sample-anatomical-source-v1 sample-local anatomical source

assay_type microarray GSE25277 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence microarray dataset_accession: GSE25277 dataset_title: Gene expression patterns of biopsies from a colonoscopy taken in 2009 of an ulcerative colitis patient infected with Trichuris trichiu... keyword match keyword match: microarray

collection_method biopsy GSM621958 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Terminal_Ileum_1_09 Amplified RNA from terminal ileum pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: terminal ileum biopsy; disease st... controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM621959 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Terminal_Ileum_2_09 Amplified RNA from terminal ileum pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: terminal ileum biopsy; disease st... controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM621960 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Ascending_Colon_1_09 Amplified RNA from ascending colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: ascending colon biopsy; disease... controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM621961 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Ascending_Colon_2_09 Amplified RNA from ascending colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: ascending colon biopsy; disease... controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM621962 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Ascending_Colon_3_09 Amplified RNA from ascending colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: ascending colon biopsy; disease... controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM621963 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Ascending_Colon_4_09 Amplified RNA from ascending colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: ascending colon biopsy; disease... controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM621964 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Transverse_Colon_1_09 Amplified RNA from transverse colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: transverse colon biopsy; dise... controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM621965 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Transverse_Colon_2_09 Amplified RNA from transverse colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: transverse colon biopsy; dise... controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM621966 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Transverse_Colon_3_09 Amplified RNA from transverse colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: transverse colon biopsy; dise... controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM621967 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Sigmoid_Colon_1_09 Amplified RNA from sigmoid colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: sigmoid colon biopsy; disease state... controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM621968 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Sigmoid_Colon_2_09 Amplified RNA from sigmoid colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: sigmoid colon biopsy; disease state... controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM621969 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Sigmoid_Colon_3_09 Amplified RNA from sigmoid colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: sigmoid colon biopsy; disease state... controlled vocabulary controlled vocabulary collection method match: biopsy

disease inflammatory bowel disease GSE25277 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence inflammatory bowel dataset_accession: GSE25277 dataset_title: Gene expression patterns of biopsies from a colonoscopy taken in 2009 of an ulcerative colitis patient infected with Trichuris trichiu... controlled vocabulary controlled vocabulary disease match: inflammatory bowel

disease ulcerative colitis GSE25277 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis dataset_accession: GSE25277 dataset_title: Gene expression patterns of biopsies from a colonoscopy taken in 2009 of an ulcerative colitis patient infected with Trichuris trichiu... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM621958 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Terminal_Ileum_1_09 Amplified RNA from terminal ileum pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: terminal ileum biopsy; disease st... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM621959 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Terminal_Ileum_2_09 Amplified RNA from terminal ileum pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: terminal ileum biopsy; disease st... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM621960 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Ascending_Colon_1_09 Amplified RNA from ascending colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: ascending colon biopsy; disease... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM621961 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Ascending_Colon_2_09 Amplified RNA from ascending colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: ascending colon biopsy; disease... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM621962 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Ascending_Colon_3_09 Amplified RNA from ascending colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: ascending colon biopsy; disease... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM621963 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Ascending_Colon_4_09 Amplified RNA from ascending colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: ascending colon biopsy; disease... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM621964 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Transverse_Colon_1_09 Amplified RNA from transverse colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: transverse colon biopsy; dise... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM621965 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Transverse_Colon_2_09 Amplified RNA from transverse colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: transverse colon biopsy; dise... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM621966 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Transverse_Colon_3_09 Amplified RNA from transverse colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: transverse colon biopsy; dise... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM621967 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Sigmoid_Colon_1_09 Amplified RNA from sigmoid colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: sigmoid colon biopsy; disease state... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM621968 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Sigmoid_Colon_2_09 Amplified RNA from sigmoid colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: sigmoid colon biopsy; disease state... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM621969 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis Sigmoid_Colon_3_09 Amplified RNA from sigmoid colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: sigmoid colon biopsy; disease state... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

organism Homo sapiens GSE25277 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE25277 dataset_title: Gene expression patterns of biopsies from a colonoscopy taken in 2009 of an ulcerative colitis patient infected with Trichuris trichiu... keyword match keyword match: homo sapiens

primary_tissue primary tissue GSM621958 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Terminal_Ileum_1_09 Amplified RNA from terminal ileum pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: terminal ileum biopsy; disease st... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM621959 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Terminal_Ileum_2_09 Amplified RNA from terminal ileum pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: terminal ileum biopsy; disease st... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM621960 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Ascending_Colon_1_09 Amplified RNA from ascending colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: ascending colon biopsy; disease... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM621961 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Ascending_Colon_2_09 Amplified RNA from ascending colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: ascending colon biopsy; disease... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM621962 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Ascending_Colon_3_09 Amplified RNA from ascending colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: ascending colon biopsy; disease... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM621963 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Ascending_Colon_4_09 Amplified RNA from ascending colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: ascending colon biopsy; disease... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM621964 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Transverse_Colon_1_09 Amplified RNA from transverse colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: transverse colon biopsy; dise... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM621965 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Transverse_Colon_2_09 Amplified RNA from transverse colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: transverse colon biopsy; dise... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM621966 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Transverse_Colon_3_09 Amplified RNA from transverse colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: transverse colon biopsy; dise... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM621967 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Sigmoid_Colon_1_09 Amplified RNA from sigmoid colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: sigmoid colon biopsy; disease state... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM621968 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Sigmoid_Colon_2_09 Amplified RNA from sigmoid colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: sigmoid colon biopsy; disease state... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM621969 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy Sigmoid_Colon_3_09 Amplified RNA from sigmoid colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: sigmoid colon biopsy; disease state... controlled vocabulary controlled vocabulary primary tissue match: biopsy

tissue colon GSE25277 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon dataset_accession: GSE25277 dataset_title: Gene expression patterns of biopsies from a colonoscopy taken in 2009 of an ulcerative colitis patient infected with Trichuris trichiu... controlled vocabulary controlled vocabulary tissue match: colon

tissue intestine GSE25277 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence intestine dataset_accession: GSE25277 dataset_title: Gene expression patterns of biopsies from a colonoscopy taken in 2009 of an ulcerative colitis patient infected with Trichuris trichiu... controlled vocabulary controlled vocabulary tissue match: intestine

tissue intestine GSM621958 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ileum Terminal_Ileum_1_09 Amplified RNA from terminal ileum pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: terminal ileum biopsy; disease st... controlled vocabulary controlled vocabulary tissue match: ileum

tissue intestine GSM621959 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence ileum Terminal_Ileum_2_09 Amplified RNA from terminal ileum pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: terminal ileum biopsy; disease st... controlled vocabulary controlled vocabulary tissue match: ileum

tissue colon GSM621960 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Ascending_Colon_1_09 Amplified RNA from ascending colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: ascending colon biopsy; disease... controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM621961 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Ascending_Colon_2_09 Amplified RNA from ascending colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: ascending colon biopsy; disease... controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM621962 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Ascending_Colon_3_09 Amplified RNA from ascending colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: ascending colon biopsy; disease... controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM621963 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Ascending_Colon_4_09 Amplified RNA from ascending colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: ascending colon biopsy; disease... controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM621964 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Transverse_Colon_1_09 Amplified RNA from transverse colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: transverse colon biopsy; dise... controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM621965 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Transverse_Colon_2_09 Amplified RNA from transverse colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: transverse colon biopsy; dise... controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM621966 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Transverse_Colon_3_09 Amplified RNA from transverse colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: transverse colon biopsy; dise... controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM621967 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Sigmoid_Colon_1_09 Amplified RNA from sigmoid colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: sigmoid colon biopsy; disease state... controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM621968 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Sigmoid_Colon_2_09 Amplified RNA from sigmoid colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: sigmoid colon biopsy; disease state... controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM621969 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon Sigmoid_Colon_3_09 Amplified RNA from sigmoid colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura tissue: sigmoid colon biopsy; disease state... controlled vocabulary controlled vocabulary tissue match: colon

Sample Group Preview

12 rows shown Show Hide

Study totals: Case 12 | Control 0 | Unassigned 0 | Excluded 0 | Ambiguous 0 12 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Ulcerative colitis	Case	GSM621958	Terminal_Ileum_1_09	Amplified RNA from terminal ileum pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura Tissue: Terminal ileum biopsy; Disease state: Ulcerative colitis patient infected with Trichuris trichiura	Case marker detected.
Ulcerative colitis	Case	GSM621959	Terminal_Ileum_2_09	Amplified RNA from terminal ileum pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura Tissue: Terminal ileum biopsy; Disease state: Ulcerative colitis patient infected with Trichuris trichiura	Case marker detected.
Ulcerative colitis	Case	GSM621960	Ascending_Colon_1_09	Amplified RNA from ascending colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura Tissue: Ascending colon biopsy; Disease state: Ulcerative colitis patient infected with Trichuris trichiura	Case marker detected.
Ulcerative colitis	Case	GSM621961	Ascending_Colon_2_09	Amplified RNA from ascending colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura Tissue: Ascending colon biopsy; Disease state: Ulcerative colitis patient infected with Trichuris trichiura	Case marker detected.
Ulcerative colitis	Case	GSM621962	Ascending_Colon_3_09	Amplified RNA from ascending colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura Tissue: Ascending colon biopsy; Disease state: Ulcerative colitis patient infected with Trichuris trichiura	Case marker detected.
Ulcerative colitis	Case	GSM621963	Ascending_Colon_4_09	Amplified RNA from ascending colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura Tissue: Ascending colon biopsy; Disease state: Ulcerative colitis patient infected with Trichuris trichiura	Case marker detected.
Ulcerative colitis	Case	GSM621964	Transverse_Colon_1_09	Amplified RNA from transverse colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura Tissue: Transverse colon biopsy; Disease state: Ulcerative colitis patient infected with Trichuris trichiura	Case marker detected.
Ulcerative colitis	Case	GSM621965	Transverse_Colon_2_09	Amplified RNA from transverse colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura Tissue: Transverse colon biopsy; Disease state: Ulcerative colitis patient infected with Trichuris trichiura	Case marker detected.
Ulcerative colitis	Case	GSM621966	Transverse_Colon_3_09	Amplified RNA from transverse colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura Tissue: Transverse colon biopsy; Disease state: Ulcerative colitis patient infected with Trichuris trichiura	Case marker detected.
Ulcerative colitis	Case	GSM621967	Sigmoid_Colon_1_09	Amplified RNA from sigmoid colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura Tissue: Sigmoid colon biopsy; Disease state: Ulcerative colitis patient infected with Trichuris trichiura	Case marker detected.
Ulcerative colitis	Case	GSM621968	Sigmoid_Colon_2_09	Amplified RNA from sigmoid colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura Tissue: Sigmoid colon biopsy; Disease state: Ulcerative colitis patient infected with Trichuris trichiura	Case marker detected.
Ulcerative colitis	Case	GSM621969	Sigmoid_Colon_3_09	Amplified RNA from sigmoid colon pinch biopsy from an ulcerative colitis patient infected with Trichuris trichiura Tissue: Sigmoid colon biopsy; Disease state: Ulcerative colitis patient infected with Trichuris trichiura	Case 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