GSE83982

Differentially expressed Transcribed ultraconserved regions (T-UCRs) in Crohn's disease (CD) comparing to normal controls (NC)

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

3 case / 3 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: 6 samples
Specimen: Biopsy
Reported/interpreted study design: Disease/model vs control Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Qian X, Shen J, Ran Z
Contact name: Xiaoxian Qian
Submission date: 2016-07-04
Last update: 2016-07-07
Organization: Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University
Department: Gastroenterology and Hepatology
Public date: 2016-07-05
Experiment types: Expression profiling by array
Platforms: GPL18564 Arraystar Human T-UCR Microarray [Agilent-038545]
Series type: Series
SubSeries: Not available
BioProject: PRJNA327742

Summary

To date, 481 transcribed ultraconserved regions (T-UCRs) have been discovered in human genome. We aimed to investigate their characteristics in Crohn’s disease (CD) with conparison to healthy normal controls, to reveal differentially expressed T-UCRs.

Overall design

3 CD patients and 3 NC volunteers were recruited in this study. With colonoscopy, colon mocosa pinch biopsy samles were got at inflammed site in CD patients and normal sites in NC volunteers respectively.

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 6 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 Crohn's disease Disease context came from Normalization rules.
Likely case group Crohn's disease 3 samples
Likely control group Healthy control 3 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: Crohn's disease.
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.
Overall score capped because comparison suitability is weak for the selected search intent.
Overall score capped because fewer than ten samples limit cohort confidence.
Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

Microarray expression context was detected; compare separately from RNA-seq cohorts.
Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.

Normalized Fields

40 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source colon GSM2224838 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue type: inflammed colon mucosa pinch biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM2224838 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon mucosa tissue type: inflammed colon mucosa pinch biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2224839 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue type: inflammed colon mucosa pinch biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM2224839 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon mucosa tissue type: inflammed colon mucosa pinch biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2224840 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue type: inflammed colon mucosa pinch biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM2224840 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon mucosa tissue type: inflammed colon mucosa pinch biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2224841 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue type: normal colon mucosa pinch biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM2224841 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon mucosa tissue type: normal colon mucosa pinch biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2224842 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue type: normal colon mucosa pinch biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM2224842 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon mucosa tissue type: normal colon mucosa pinch biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon GSM2224843 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon tissue type: normal colon mucosa pinch biopsy sample-anatomical-source-v1 sample-local anatomical source

anatomical_source colon mucosa GSM2224843 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence colon mucosa tissue type: normal colon mucosa pinch biopsy sample-anatomical-source-v1 sample-local anatomical source

assay_type microarray GSE83982 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence microarray dataset_accession: GSE83982 dataset_title: Differentially expressed Transcribed ultraconserved regions (T-UCRs) in Crohn's disease (CD) comparing to normal controls (NC) organis... keyword match keyword match: microarray

collection_method biopsy GSM2224838 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy CD-1 inflammed colon mucosa pinch biopsy sample under colonoscopy in CD patients subject status: Crohn's disease (CD) patient; tag: colon; tissue type: inflammed colon mucosa pi... controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM2224839 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy CD-2 inflammed colon mucosa pinch biopsy sample under colonoscopy in CD patients subject status: Crohn's disease (CD) patient; tag: colon; tissue type: inflammed colon mucosa pi... controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM2224840 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy CD-3 inflammed colon mucosa pinch biopsy sample under colonoscopy in CD patients subject status: Crohn's disease (CD) patient; tag: colon; tissue type: inflammed colon mucosa pi... controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM2224841 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy NC-1 normal colon mucosa pinch biopsy sample under colonoscopy in NC volunteers subject status: normal controls (NC) volunteer; tag: colon; tissue type: normal colon mucosa pinc... controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM2224842 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy NC-2 normal colon mucosa pinch biopsy sample under colonoscopy in NC volunteers subject status: normal controls (NC) volunteer; tag: colon; tissue type: normal colon mucosa pinc... controlled vocabulary controlled vocabulary collection method match: biopsy

collection_method biopsy GSM2224843 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy NC-3 normal colon mucosa pinch biopsy sample under colonoscopy in NC volunteers subject status: normal controls (NC) volunteer; tag: colon; tissue type: normal colon mucosa pinc... controlled vocabulary controlled vocabulary collection method match: biopsy

disease Crohn's disease GSE83982 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease dataset_accession: GSE83982 dataset_title: Differentially expressed Transcribed ultraconserved regions (T-UCRs) in Crohn's disease (CD) comparing to normal controls (NC) organis... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2224838 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease CD-1 inflammed colon mucosa pinch biopsy sample under colonoscopy in CD patients subject status: Crohn's disease (CD) patient; tag: colon; tissue type: inflammed colon mucosa pi... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2224839 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease CD-2 inflammed colon mucosa pinch biopsy sample under colonoscopy in CD patients subject status: Crohn's disease (CD) patient; tag: colon; tissue type: inflammed colon mucosa pi... controlled vocabulary controlled vocabulary disease match: Crohn's disease

disease Crohn's disease GSM2224840 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence Crohn's disease CD-3 inflammed colon mucosa pinch biopsy sample under colonoscopy in CD patients subject status: Crohn's disease (CD) patient; tag: colon; tissue type: inflammed colon mucosa pi... controlled vocabulary controlled vocabulary disease match: Crohn's disease

organism Homo sapiens GSE83982 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE83982 dataset_title: Differentially expressed Transcribed ultraconserved regions (T-UCRs) in Crohn's disease (CD) comparing to normal controls (NC) organis... keyword match keyword match: homo sapiens

primary_tissue primary tissue GSM2224838 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy CD-1 inflammed colon mucosa pinch biopsy sample under colonoscopy in CD patients subject status: Crohn's disease (CD) patient; tag: colon; tissue type: inflammed colon mucosa pi... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM2224839 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy CD-2 inflammed colon mucosa pinch biopsy sample under colonoscopy in CD patients subject status: Crohn's disease (CD) patient; tag: colon; tissue type: inflammed colon mucosa pi... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM2224840 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy CD-3 inflammed colon mucosa pinch biopsy sample under colonoscopy in CD patients subject status: Crohn's disease (CD) patient; tag: colon; tissue type: inflammed colon mucosa pi... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM2224841 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy NC-1 normal colon mucosa pinch biopsy sample under colonoscopy in NC volunteers subject status: normal controls (NC) volunteer; tag: colon; tissue type: normal colon mucosa pinc... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM2224842 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy NC-2 normal colon mucosa pinch biopsy sample under colonoscopy in NC volunteers subject status: normal controls (NC) volunteer; tag: colon; tissue type: normal colon mucosa pinc... controlled vocabulary controlled vocabulary primary tissue match: biopsy

primary_tissue primary tissue GSM2224843 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence biopsy NC-3 normal colon mucosa pinch biopsy sample under colonoscopy in NC volunteers subject status: normal controls (NC) volunteer; tag: colon; tissue type: normal colon mucosa pinc... controlled vocabulary controlled vocabulary primary tissue match: biopsy

sample_type normal tissue GSM2224841 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal NC-1 normal colon mucosa pinch biopsy sample under colonoscopy in NC volunteers subject status: normal controls (NC) volunteer; tag: colon; tissue type: normal colon mucosa pinc... controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM2224842 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal NC-2 normal colon mucosa pinch biopsy sample under colonoscopy in NC volunteers subject status: normal controls (NC) volunteer; tag: colon; tissue type: normal colon mucosa pinc... controlled vocabulary controlled vocabulary sample type match: normal

sample_type normal tissue GSM2224843 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence normal NC-3 normal colon mucosa pinch biopsy sample under colonoscopy in NC volunteers subject status: normal controls (NC) volunteer; tag: colon; tissue type: normal colon mucosa pinc... controlled vocabulary controlled vocabulary sample type match: normal

tissue colon GSE83982 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon dataset_accession: GSE83982 dataset_title: Differentially expressed Transcribed ultraconserved regions (T-UCRs) in Crohn's disease (CD) comparing to normal controls (NC) organis... controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2224838 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon CD-1 inflammed colon mucosa pinch biopsy sample under colonoscopy in CD patients subject status: Crohn's disease (CD) patient; tag: colon; tissue type: inflammed colon mucosa pi... controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2224839 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon CD-2 inflammed colon mucosa pinch biopsy sample under colonoscopy in CD patients subject status: Crohn's disease (CD) patient; tag: colon; tissue type: inflammed colon mucosa pi... controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2224840 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon CD-3 inflammed colon mucosa pinch biopsy sample under colonoscopy in CD patients subject status: Crohn's disease (CD) patient; tag: colon; tissue type: inflammed colon mucosa pi... controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2224841 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon NC-1 normal colon mucosa pinch biopsy sample under colonoscopy in NC volunteers subject status: normal controls (NC) volunteer; tag: colon; tissue type: normal colon mucosa pinc... controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2224842 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon NC-2 normal colon mucosa pinch biopsy sample under colonoscopy in NC volunteers subject status: normal controls (NC) volunteer; tag: colon; tissue type: normal colon mucosa pinc... controlled vocabulary controlled vocabulary tissue match: colon

tissue colon GSM2224843 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence colon NC-3 normal colon mucosa pinch biopsy sample under colonoscopy in NC volunteers subject status: normal controls (NC) volunteer; tag: colon; tissue type: normal colon mucosa pinc... controlled vocabulary controlled vocabulary tissue match: colon

Sample Group Preview

6 rows shown Show Hide

Study totals: Case 3 | Control 3 | Unassigned 0 | Excluded 0 | Ambiguous 0 6 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Crohn's disease	Case	GSM2224838	CD-1	Inflammed colon mucosa pinch biopsy sample under colonoscopy in CD patients Subject status: Crohn's disease (CD) patient; Tag: Colon; Tissue type: Inflammed colon mucosa pinch biopsy	Case marker detected.
Crohn's disease	Case	GSM2224839	CD-2	Inflammed colon mucosa pinch biopsy sample under colonoscopy in CD patients Subject status: Crohn's disease (CD) patient; Tag: Colon; Tissue type: Inflammed colon mucosa pinch biopsy	Case marker detected.
Crohn's disease	Case	GSM2224840	CD-3	Inflammed colon mucosa pinch biopsy sample under colonoscopy in CD patients Subject status: Crohn's disease (CD) patient; Tag: Colon; Tissue type: Inflammed colon mucosa pinch biopsy	Case marker detected.
Healthy control	Control	GSM2224841	NC-1	Normal colon mucosa pinch biopsy sample under colonoscopy in NC volunteers Subject status: Normal controls (NC) volunteer; Tag: Colon; Tissue type: Normal colon mucosa pinch biopsy	Sample-local control marker detected.
Healthy control	Control	GSM2224842	NC-2	Normal colon mucosa pinch biopsy sample under colonoscopy in NC volunteers Subject status: Normal controls (NC) volunteer; Tag: Colon; Tissue type: Normal colon mucosa pinch biopsy	Sample-local control marker detected.
Healthy control	Control	GSM2224843	NC-3	Normal colon mucosa pinch biopsy sample under colonoscopy in NC volunteers Subject status: Normal controls (NC) volunteer; Tag: Colon; Tissue type: Normal colon mucosa pinch biopsy	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.