GSE131911

Expression Profiles of Circular RNAs in colon biopsies from Crohn’s Disease Patients by Microarray Analysis

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

8 case / 4 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
Unclear specimen/source
Reported/interpreted study design
Disease/model vs control Design classification does not establish patient pairs.
Comparison type
Tumor vs normal
Contributors
Hu Y, Zhu Y, Li X
Contact name
Xiaojun LI
Submission date
2019-05-29
Last update
2019-06-01
Organization
Jinling Hospital, Nanjing University School of Medicine
Department
Institute of Clinical Laboratory Science,
Public date
2019-05-30
Experiment types
Non-coding RNA profiling by array
Platforms
GPL21825 074301 Arraystar Human CircRNA microarray V2
Series type
Series
SubSeries
Not available
BioProject
PRJNA545304

Summary

To investigate the expression profiles of circRNAs in colon tissues of the patients with Crohn’s Disease(CD) , ulcerative colitis (UC) and healthy controls (HC), we used circRNA microArray analysis form Arraystar to examine the expression of circRNAs in colon tissues of CD,UC and HC.

Overall design

12 pinch tissues of colonic biopsies from 4 CD patients, 4 UC patients and 4 healthy controls were conducted with Human circRNA Array v2.0 microarray (8×15K, Arraystar) to acquire expression profiles.

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

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

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 Crohn's disease, ulcerative colitis Disease context came from Normalization rules.
  • Likely case group Ulcerative colitis 8 samples
  • Likely control group Healthy control 4 samples

Intent Interpretation

  • Downgrade or exclusion reason Comparison: Disease/model vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

  • Interpreted disease metadata: Crohn's disease, Ulcerative colitis.
  • Processed data is available for downstream review.

Cautions

  • Comparison: Disease/model vs control. Specimen: Unclear specimen/source. 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.
  • Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
  • Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
  • Missing or unclear metadata. Unclear specimen/source downgraded for patient tissue tumor-vs-normal search intent.
  • 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.
  • Missing or unclear metadata. Comparison - Disease/model vs control. Specimen - Unclear specimen/source. 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

Normalized Fields

13 fields

Sample Group Preview

12 rows shown Show Hide
Study totals: Case 8 | Control 4 | Unassigned 0 | Excluded 0 | Ambiguous 0 12 rows shown
Group Role Accession Title Source / characteristics Reason
Ulcerative colitis Case GSM3827177 Patient 1 ulcerative colitis01 Ulcerative colitis Age: 48; Sex: Female Case marker detected.
Ulcerative colitis Case GSM3827178 Patient 2 ulcerative colitis02 Ulcerative colitis Age: 51; Sex: Male Case marker detected.
Ulcerative colitis Case GSM3827179 Patient 3 ulcerative colitis03 Ulcerative colitis Age: 53; Sex: Male Case marker detected.
Ulcerative colitis Case GSM3827180 Patient 4 ulcerative colitis04 Ulcerative colitis Age: 36; Sex: Male Case marker detected.
Crohn's disease Case GSM3827181 Patient 5 Crohn’s Disease01 Crohn’s Disease Age: 38; Sex: Female Case marker detected.
Crohn's disease Case GSM3827182 Patient 6 Crohn’s Disease02 Crohn’s Disease Age: 43; Sex: Male Case marker detected.
Crohn's disease Case GSM3827183 Patient 7 Crohn’s Disease03 Crohn’s Disease Age: 29; Sex: Male Case marker detected.
Crohn's disease Case GSM3827184 Patient 8 Crohn’s Disease04 Crohn’s Disease Age: 47; Sex: Female Case marker detected.
Healthy control Control GSM3827185 Healthy control01 Healthy controls Age: 47; Sex: Female Sample-local control marker detected.
Healthy control Control GSM3827186 Healthy control02 Healthy controls Age: 49; Sex: Female Sample-local control marker detected.
Healthy control Control GSM3827187 Healthy control03 Healthy controls Age: 38; Sex: Male Sample-local control marker detected.
Healthy control Control GSM3827188 Healthy control04 Healthy controls Age: 50; Sex: Male 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.