GSE48958

Mucosal gene expression profiling in (un)inflamed colon of patients with ulcerative colitis (UC)

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

13 case / 8 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: 21 samples
Specimen: Biopsy
Reported/interpreted study design: Disease/model vs control Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Van der Goten J, Van Lommel L, Ferrante M, Van Assche G, Rutgeerts P, Schuit F, Vermeire S, Arijs I
Contact name: Jan Van der Goten
Submission date: 2013-07-17
Last update: 2018-07-26
Organization: KU Leuven
Department: Clinical and Experimental Medicine
Public date: 2015-01-01
Experiment types: Expression profiling by array
Platforms: GPL6244 [HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]
Series type: SubSeries
SubSeries: Not available
BioProject: PRJNA212400

Summary

In this study, we investigated if miRNA expression in UC mucosa is altered and correlated our findings with mucosal mRNA expression. Integration of mRNA and miRNA expression profiling may allow the identification of functional links between dysregulated miRNAs and their predicted target mRNA.

Overall design

Colonic mucosal biopsies were obtained during endoscopy from 13 UC (7 active and 6 inactive) patients and 8 normal controls. Total RNA was isolated from colonic mucosal biopsies, labelled and hybridized to Affymetrix Genechip Human Gene 1.0ST Arrays.

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 21 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. 12 linked publications 11 DOIs Primary publication Integrated miRNA and mRNA expression profiling in inflamed colon of patients with ulcerative colitis. PloS one, 2014 PubMed DOI Related publications Integrative computational approach identifies immune-relevant biomarkers in ulcerative colitis. FEBS open bio, 2022 PubMed DOI The critical role of COL1A1 revealed by integrated bioinformatics analysis of differentially-expressed genes in colorectal cancer and inflammatory bowel disease. Computers in biology and medicine, 2025 PubMed DOI Identification of cholesterol homeostasis related genes and potential pathogenesis mechanisms in ulcerative colitis. The Journal of steroid biochemistry and molecular biology, 2025 PubMed DOI Study on the mechanism of action of HuaZhuoKeLi in modulating LCN2-mediated cellular pyroptosis to ameliorate ulcerative colitis. Scientific reports, 2026 PubMed DOI Identification of Differential Intestinal Mucosa Transcriptomic Biomarkers for Ulcerative Colitis by Bioinformatics Analysis. Disease markers, 2020 PubMed DOI Bioinformatics Analysis of Differentially Expressed Genes and Protein-Protein Interaction Networks Associated with Functional Pathways in Ulcerative Colitis. Medical science monitor : international medical journal of experimental and clinical research, 2021 PubMed DOI Identification and Experimental Validation of Oxidative Stress-Related Biomarkers in Ulcerative Colitis Using Machine Learning. Journal of inflammation research, 2025 PubMed DOI Identification of Differentially Expressed Genes and miRNAs for Ulcerative Colitis Using Bioinformatics Analysis. Frontiers in genetics, 2022 PubMed DOI Exploring the molecular characteristics of inflammatory bowel disease from the perspective of hypoxia-related genes. Frontiers in pharmacology, 2025 PubMed DOI Integrated Metabolomic and Transcriptomic Analyses Reveal Alterations in the Serotonergic Synapse Pathway and a Robust Diagnostic Model in Ulcerative Colitis. Metabolites, 2026 PubMed DOI Identification of Crucial Genes and Related Transcription Factors in Ulcerative Colitis. Annals of clinical and laboratory science, 2021 PubMed	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

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

Secondary RNA assay context should be analyzed separately from ordinary bulk RNA-seq.

Next Steps

Review blockers and update sample grouping or dataset selection before analysis.

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.

Analysis readiness has blockers that must be resolved 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 13 samples
Likely control group Control 8 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: Biopsy. Comparison suitability: 0%.
Interpreted disease metadata: Ulcerative colitis.
Processed data is available for downstream review.
External evidence: PubMed links 12 publications; 11 DOIs available: PMID 25546151, PMID 33144895, PMID 33462173, PMID 33941565, PMID 34939750.
Publication context: Integrated miRNA and mRNA expression profiling in inflamed colon of patients with ulcerative colitis.. PloS one, 2014. PMID 25546151. DOI 10.1371/journal.pone.0116117.
Publication context: Identification of Differential Intestinal Mucosa Transcriptomic Biomarkers for Ulcerative Colitis by Bioinformatics Analysis.. Disease markers, 2020. PMID 33144895. DOI 10.1155/2020/8876565.
Publication context: Bioinformatics Analysis of Differentially Expressed Genes and Protein-Protein Interaction Networks Associated with Functional Pathways in Ulcerative Colitis.. Medical science monitor : international medical journal of experimental and clinical research, 2021. PMID 33462173. DOI 10.12659/MSM.927917.
Publication context: 9 additional linked PubMed publications are available.

Cautions

Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA 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

Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
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

101 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source colon GSM1187602 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1187603 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1187604 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1187605 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1187606 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1187607 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1187608 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1187609 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1187610 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1187611 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1187612 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1187613 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1187614 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1187615 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1187616 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1187617 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1187618 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1187619 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1187620 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1187621 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM1187622 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue: colon sample-anatomical-source-v1 sample-local anatomical source

assay_type microarray GSE48958 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence microarray dataset_accession: GSE48958 dataset_title: Mucosal gene expression profiling in (un)inflamed colon of patients with ulcerative colitis (UC) organism: Homo sapiens assay_type: mi... keyword match keyword match: microarray

collection_method biopsy GSM1187602 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy control_1 [mRNA] colonic mucosal biopsy from control individual tissue: colon; disease: control; disease activity: not applicable controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1187603 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy control_2 [mRNA] colonic mucosal biopsy from control individual tissue: colon; disease: control; disease activity: not applicable controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1187604 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy control_3 [mRNA] colonic mucosal biopsy from control individual tissue: colon; disease: control; disease activity: not applicable controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1187605 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy control_4 [mRNA] colonic mucosal biopsy from control individual tissue: colon; disease: control; disease activity: not applicable controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1187606 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy control_5 [mRNA] colonic mucosal biopsy from control individual tissue: colon; disease: control; disease activity: not applicable controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1187607 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy control_7 [mRNA] colonic mucosal biopsy from control individual tissue: colon; disease: control; disease activity: not applicable controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1187608 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy control_8 [mRNA] colonic mucosal biopsy from control individual tissue: colon; disease: control; disease activity: not applicable controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1187609 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy control_10 [mRNA] colonic mucosal biopsy from control individual tissue: colon; disease: control; disease activity: not applicable controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1187610 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy UC_active_1 [mRNA] colonic mucosal biopsy from UC patient with active disease tissue: colon; disease: UC; disease activity: active controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1187611 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy UC_active_2 [mRNA] colonic mucosal biopsy from UC patient with active disease tissue: colon; disease: UC; disease activity: active controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1187612 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy UC_active_3 [mRNA] colonic mucosal biopsy from UC patient with active disease tissue: colon; disease: UC; disease activity: active controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1187613 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy UC_active_4 [mRNA] colonic mucosal biopsy from UC patient with active disease tissue: colon; disease: UC; disease activity: active controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1187614 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy UC_active_6 [mRNA] colonic mucosal biopsy from UC patient with active disease tissue: colon; disease: UC; disease activity: active controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1187615 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy UC_active_7 [mRNA] colonic mucosal biopsy from UC patient with active disease tissue: colon; disease: UC; disease activity: active controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1187616 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy UC_active_9 [mRNA] colonic mucosal biopsy from UC patient with active disease tissue: colon; disease: UC; disease activity: active controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1187617 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy UC_inactive_1 [mRNA] colonic mucosal biopsy from UC patient with inactive disease tissue: colon; disease: UC; disease activity: inactive controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1187618 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy UC_inactive_2 [mRNA] colonic mucosal biopsy from UC patient with inactive disease tissue: colon; disease: UC; disease activity: inactive controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1187619 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy UC_inactive_3 [mRNA] colonic mucosal biopsy from UC patient with inactive disease tissue: colon; disease: UC; disease activity: inactive controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1187620 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy UC_inactive_4 [mRNA] colonic mucosal biopsy from UC patient with inactive disease tissue: colon; disease: UC; disease activity: inactive controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1187621 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy UC_inactive_5 [mRNA] colonic mucosal biopsy from UC patient with inactive disease tissue: colon; disease: UC; disease activity: inactive controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM1187622 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy UC_inactive_6 [mRNA] colonic mucosal biopsy from UC patient with inactive disease tissue: colon; disease: UC; disease activity: inactive controlled vocabulary controlled vocabulary collection method match: biopsy

disease ulcerative colitis GSE48958 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence ulcerative colitis dataset_accession: GSE48958 dataset_title: Mucosal gene expression profiling in (un)inflamed colon of patients with ulcerative colitis (UC) organism: Homo sapiens assay_type: mi... controlled vocabulary controlled vocabulary disease match: ulcerative colitis

disease ulcerative colitis GSM1187610 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC UC_active_1 [mRNA] colonic mucosal biopsy from UC patient with active disease tissue: colon; disease: UC; disease activity: active controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM1187611 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC UC_active_2 [mRNA] colonic mucosal biopsy from UC patient with active disease tissue: colon; disease: UC; disease activity: active controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM1187612 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC UC_active_3 [mRNA] colonic mucosal biopsy from UC patient with active disease tissue: colon; disease: UC; disease activity: active controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM1187613 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC UC_active_4 [mRNA] colonic mucosal biopsy from UC patient with active disease tissue: colon; disease: UC; disease activity: active controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM1187614 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC UC_active_6 [mRNA] colonic mucosal biopsy from UC patient with active disease tissue: colon; disease: UC; disease activity: active controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM1187615 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC UC_active_7 [mRNA] colonic mucosal biopsy from UC patient with active disease tissue: colon; disease: UC; disease activity: active controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM1187616 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC UC_active_9 [mRNA] colonic mucosal biopsy from UC patient with active disease tissue: colon; disease: UC; disease activity: active controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM1187617 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC UC_inactive_1 [mRNA] colonic mucosal biopsy from UC patient with inactive disease tissue: colon; disease: UC; disease activity: inactive controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM1187618 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC UC_inactive_2 [mRNA] colonic mucosal biopsy from UC patient with inactive disease tissue: colon; disease: UC; disease activity: inactive controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM1187619 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC UC_inactive_3 [mRNA] colonic mucosal biopsy from UC patient with inactive disease tissue: colon; disease: UC; disease activity: inactive controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM1187620 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC UC_inactive_4 [mRNA] colonic mucosal biopsy from UC patient with inactive disease tissue: colon; disease: UC; disease activity: inactive controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM1187621 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC UC_inactive_5 [mRNA] colonic mucosal biopsy from UC patient with inactive disease tissue: colon; disease: UC; disease activity: inactive controlled vocabulary controlled vocabulary disease match: UC

disease ulcerative colitis GSM1187622 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence UC UC_inactive_6 [mRNA] colonic mucosal biopsy from UC patient with inactive disease tissue: colon; disease: UC; disease activity: inactive controlled vocabulary controlled vocabulary disease match: UC

organism Homo sapiens GSE48958 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE48958 dataset_title: Mucosal gene expression profiling in (un)inflamed colon of patients with ulcerative colitis (UC) organism: Homo sapiens assay_type: mi... keyword match keyword match: homo sapiens

primary_tissue primary tissue GSM1187602 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy control_1 [mRNA] colonic mucosal biopsy from control individual tissue: colon; disease: control; disease activity: not applicable controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1187603 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy control_2 [mRNA] colonic mucosal biopsy from control individual tissue: colon; disease: control; disease activity: not applicable controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1187604 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy control_3 [mRNA] colonic mucosal biopsy from control individual tissue: colon; disease: control; disease activity: not applicable controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1187605 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy control_4 [mRNA] colonic mucosal biopsy from control individual tissue: colon; disease: control; disease activity: not applicable controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1187606 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy control_5 [mRNA] colonic mucosal biopsy from control individual tissue: colon; disease: control; disease activity: not applicable controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1187607 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy control_7 [mRNA] colonic mucosal biopsy from control individual tissue: colon; disease: control; disease activity: not applicable controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1187608 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy control_8 [mRNA] colonic mucosal biopsy from control individual tissue: colon; disease: control; disease activity: not applicable controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1187609 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy control_10 [mRNA] colonic mucosal biopsy from control individual tissue: colon; disease: control; disease activity: not applicable controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1187610 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy UC_active_1 [mRNA] colonic mucosal biopsy from UC patient with active disease tissue: colon; disease: UC; disease activity: active controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1187611 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy UC_active_2 [mRNA] colonic mucosal biopsy from UC patient with active disease tissue: colon; disease: UC; disease activity: active controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1187612 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy UC_active_3 [mRNA] colonic mucosal biopsy from UC patient with active disease tissue: colon; disease: UC; disease activity: active controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1187613 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy UC_active_4 [mRNA] colonic mucosal biopsy from UC patient with active disease tissue: colon; disease: UC; disease activity: active controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1187614 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy UC_active_6 [mRNA] colonic mucosal biopsy from UC patient with active disease tissue: colon; disease: UC; disease activity: active controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1187615 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy UC_active_7 [mRNA] colonic mucosal biopsy from UC patient with active disease tissue: colon; disease: UC; disease activity: active controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1187616 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy UC_active_9 [mRNA] colonic mucosal biopsy from UC patient with active disease tissue: colon; disease: UC; disease activity: active controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1187617 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy UC_inactive_1 [mRNA] colonic mucosal biopsy from UC patient with inactive disease tissue: colon; disease: UC; disease activity: inactive controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1187618 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy UC_inactive_2 [mRNA] colonic mucosal biopsy from UC patient with inactive disease tissue: colon; disease: UC; disease activity: inactive controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1187619 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy UC_inactive_3 [mRNA] colonic mucosal biopsy from UC patient with inactive disease tissue: colon; disease: UC; disease activity: inactive controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1187620 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy UC_inactive_4 [mRNA] colonic mucosal biopsy from UC patient with inactive disease tissue: colon; disease: UC; disease activity: inactive controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1187621 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy UC_inactive_5 [mRNA] colonic mucosal biopsy from UC patient with inactive disease tissue: colon; disease: UC; disease activity: inactive controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM1187622 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy UC_inactive_6 [mRNA] colonic mucosal biopsy from UC patient with inactive disease tissue: colon; disease: UC; disease activity: inactive controlled vocabulary controlled vocabulary primary tissue match: biopsy

tissue colon GSE48958 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon dataset_accession: GSE48958 dataset_title: Mucosal gene expression profiling in (un)inflamed colon of patients with ulcerative colitis (UC) organism: Homo sapiens assay_type: mi... controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1187602 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon control_1 [mRNA] colonic mucosal biopsy from control individual tissue: colon; disease: control; disease activity: not applicable controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1187603 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon control_2 [mRNA] colonic mucosal biopsy from control individual tissue: colon; disease: control; disease activity: not applicable controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1187604 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon control_3 [mRNA] colonic mucosal biopsy from control individual tissue: colon; disease: control; disease activity: not applicable controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1187605 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon control_4 [mRNA] colonic mucosal biopsy from control individual tissue: colon; disease: control; disease activity: not applicable controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1187606 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon control_5 [mRNA] colonic mucosal biopsy from control individual tissue: colon; disease: control; disease activity: not applicable controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1187607 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon control_7 [mRNA] colonic mucosal biopsy from control individual tissue: colon; disease: control; disease activity: not applicable controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1187608 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon control_8 [mRNA] colonic mucosal biopsy from control individual tissue: colon; disease: control; disease activity: not applicable controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1187609 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon control_10 [mRNA] colonic mucosal biopsy from control individual tissue: colon; disease: control; disease activity: not applicable controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1187610 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon UC_active_1 [mRNA] colonic mucosal biopsy from UC patient with active disease tissue: colon; disease: UC; disease activity: active controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1187611 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon UC_active_2 [mRNA] colonic mucosal biopsy from UC patient with active disease tissue: colon; disease: UC; disease activity: active controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1187612 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon UC_active_3 [mRNA] colonic mucosal biopsy from UC patient with active disease tissue: colon; disease: UC; disease activity: active controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1187613 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon UC_active_4 [mRNA] colonic mucosal biopsy from UC patient with active disease tissue: colon; disease: UC; disease activity: active controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1187614 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon UC_active_6 [mRNA] colonic mucosal biopsy from UC patient with active disease tissue: colon; disease: UC; disease activity: active controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1187615 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon UC_active_7 [mRNA] colonic mucosal biopsy from UC patient with active disease tissue: colon; disease: UC; disease activity: active controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1187616 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon UC_active_9 [mRNA] colonic mucosal biopsy from UC patient with active disease tissue: colon; disease: UC; disease activity: active controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1187617 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon UC_inactive_1 [mRNA] colonic mucosal biopsy from UC patient with inactive disease tissue: colon; disease: UC; disease activity: inactive controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1187618 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon UC_inactive_2 [mRNA] colonic mucosal biopsy from UC patient with inactive disease tissue: colon; disease: UC; disease activity: inactive controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1187619 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon UC_inactive_3 [mRNA] colonic mucosal biopsy from UC patient with inactive disease tissue: colon; disease: UC; disease activity: inactive controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1187620 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon UC_inactive_4 [mRNA] colonic mucosal biopsy from UC patient with inactive disease tissue: colon; disease: UC; disease activity: inactive controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1187621 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon UC_inactive_5 [mRNA] colonic mucosal biopsy from UC patient with inactive disease tissue: colon; disease: UC; disease activity: inactive controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM1187622 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon UC_inactive_6 [mRNA] colonic mucosal biopsy from UC patient with inactive disease tissue: colon; disease: UC; disease activity: inactive controlled vocabulary controlled vocabulary tissue match: colon

Sample Group Preview

21 rows shown Show Hide

Study totals: Case 13 | Control 8 | Unassigned 0 | Excluded 0 | Ambiguous 0 21 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Inflamed tissue	Case	GSM1187610	UC_active_1 [mRNA]	Colonic mucosal biopsy from UC patient with active disease Tissue: Colon; Disease: UC; Disease activity: Active	Explicit sample label case marker detected.
Inflamed tissue	Case	GSM1187611	UC_active_2 [mRNA]	Colonic mucosal biopsy from UC patient with active disease Tissue: Colon; Disease: UC; Disease activity: Active	Explicit sample label case marker detected.
Inflamed tissue	Case	GSM1187612	UC_active_3 [mRNA]	Colonic mucosal biopsy from UC patient with active disease Tissue: Colon; Disease: UC; Disease activity: Active	Explicit sample label case marker detected.
Inflamed tissue	Case	GSM1187613	UC_active_4 [mRNA]	Colonic mucosal biopsy from UC patient with active disease Tissue: Colon; Disease: UC; Disease activity: Active	Explicit sample label case marker detected.
Inflamed tissue	Case	GSM1187614	UC_active_6 [mRNA]	Colonic mucosal biopsy from UC patient with active disease Tissue: Colon; Disease: UC; Disease activity: Active	Explicit sample label case marker detected.
Inflamed tissue	Case	GSM1187615	UC_active_7 [mRNA]	Colonic mucosal biopsy from UC patient with active disease Tissue: Colon; Disease: UC; Disease activity: Active	Explicit sample label case marker detected.
Inflamed tissue	Case	GSM1187616	UC_active_9 [mRNA]	Colonic mucosal biopsy from UC patient with active disease Tissue: Colon; Disease: UC; Disease activity: Active	Explicit sample label case marker detected.
Ulcerative colitis	Case	GSM1187617	UC_inactive_1 [mRNA]	Colonic mucosal biopsy from UC patient with inactive disease Tissue: Colon; Disease: UC; Disease activity: Inactive	Case marker detected.
Ulcerative colitis	Case	GSM1187618	UC_inactive_2 [mRNA]	Colonic mucosal biopsy from UC patient with inactive disease Tissue: Colon; Disease: UC; Disease activity: Inactive	Case marker detected.
Ulcerative colitis	Case	GSM1187619	UC_inactive_3 [mRNA]	Colonic mucosal biopsy from UC patient with inactive disease Tissue: Colon; Disease: UC; Disease activity: Inactive	Case marker detected.
Ulcerative colitis	Case	GSM1187620	UC_inactive_4 [mRNA]	Colonic mucosal biopsy from UC patient with inactive disease Tissue: Colon; Disease: UC; Disease activity: Inactive	Case marker detected.
Ulcerative colitis	Case	GSM1187621	UC_inactive_5 [mRNA]	Colonic mucosal biopsy from UC patient with inactive disease Tissue: Colon; Disease: UC; Disease activity: Inactive	Case marker detected.
Ulcerative colitis	Case	GSM1187622	UC_inactive_6 [mRNA]	Colonic mucosal biopsy from UC patient with inactive disease Tissue: Colon; Disease: UC; Disease activity: Inactive	Case marker detected.
Control	Control	GSM1187602	Control_1 [mRNA]	Colonic mucosal biopsy from control individual Tissue: Colon; Disease: Control; Disease activity: Not applicable	Sample-local control marker detected.
Control	Control	GSM1187603	Control_2 [mRNA]	Colonic mucosal biopsy from control individual Tissue: Colon; Disease: Control; Disease activity: Not applicable	Sample-local control marker detected.
Control	Control	GSM1187604	Control_3 [mRNA]	Colonic mucosal biopsy from control individual Tissue: Colon; Disease: Control; Disease activity: Not applicable	Sample-local control marker detected.
Control	Control	GSM1187605	Control_4 [mRNA]	Colonic mucosal biopsy from control individual Tissue: Colon; Disease: Control; Disease activity: Not applicable	Sample-local control marker detected.
Control	Control	GSM1187606	Control_5 [mRNA]	Colonic mucosal biopsy from control individual Tissue: Colon; Disease: Control; Disease activity: Not applicable	Sample-local control marker detected.
Control	Control	GSM1187607	Control_7 [mRNA]	Colonic mucosal biopsy from control individual Tissue: Colon; Disease: Control; Disease activity: Not applicable	Sample-local control marker detected.
Control	Control	GSM1187608	Control_8 [mRNA]	Colonic mucosal biopsy from control individual Tissue: Colon; Disease: Control; Disease activity: Not applicable	Sample-local control marker detected.
Control	Control	GSM1187609	Control_10 [mRNA]	Colonic mucosal biopsy from control individual Tissue: Colon; Disease: Control; Disease activity: Not applicable	Sample-local control marker detected.

Use as Discovery Cohort

External Validation Finder

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

Summary

Overall design

Source Evidence

Primary publication

Related publications

Metadata Quality Components

Analysis Readiness

Blockers

Next Steps

Analysis Preparation Checklist

Bioinformatician Review

Why This Is Ranked Here

Applied Review Decisions

Derived Classifications

Intent Interpretation

Ranking Facts

Supporting evidence

Cautions

Dataset Warnings

Normalized Fields

Sample Group Preview

Use as Discovery Cohort