GSE75459

Plasma Long Noncoding RNA and mRNA Expression Profile of Crohn’s Disease identified by Microarray

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
Biofluid
Reported/interpreted study design
Disease/model vs control Design classification does not establish patient pairs.
Comparison type
Tumor vs normal
Contributors
Chen D, Jin X
Contact name
Xi Jin
Submission date
2015-11-29
Last update
2018-03-12
Organization
The First Affilated Hospital, School of Medicine, Zhejiang University
Department
Department of
Public date
2017-09-01
Experiment types
Expression profiling by array; Non-coding RNA profiling by array
Platforms
GPL16956 Agilent-045997 Arraystar human lncRNA microarray V3 (Probe Name Version)
Series type
Series
SubSeries
Not available
BioProject
PRJNA304347

Summary

We performed a genome-wide analysis of lncRNA expression to identify novel targets in Crohn's disease (CD). Samples obtained from CD patients and control were analyzed using Arraystar human 8×60K lncRNA/mRNA v3.0 microarrays chips to find differentially expressed lncRNAs and mRNAs; The results were confirmed by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). The differentially expressed lncRNAs and mRNAs were identified through fold-change filtering. Gene ontology (GO) and pathway analyses were performed using standard enrichment computational methods.

Overall design

We performed a genome-wide analysis of lncRNA expression to identify novel targets for the further study of Crohn's disease. 3 CD samples(D1-3) and 3 control samples (C1-3) were obtained .

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

Primary GEO citations and related PubMed articles that mention this dataset.

1 linked publication 1 DOI

Primary publication

  1. Plasma long noncoding RNA expression profile identified by microarray in patients with Crohn's disease. World journal of gastroenterology, 2016
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 Crohn's disease Disease context came from Normalization rules.
  • Likely case group Crohn's disease 3 samples
  • Likely control group Control 3 samples

Intent Interpretation

  • Downgrade or exclusion reason Downgraded for tissue search because it is a biofluid cohort. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

  • Comparison: Disease/model vs control. Specimen: Biofluid. Comparison suitability: 0%.
  • Interpreted disease metadata: Crohn's disease.
  • Processed data is available for downstream review.
  • External evidence: PubMed links 1 publication; 1 DOI available: PMID 27217703.
  • Publication context: Plasma long noncoding RNA expression profile identified by microarray in patients with Crohn's disease.. World journal of gastroenterology, 2016. PMID 27217703. DOI 10.3748/wjg.v22.i19.4716.

Cautions

  • Downgraded for tissue search because it is a biofluid cohort.
  • Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
  • Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
  • Blood, plasma, or serum cohort downgraded because this ranking targets tissue tumor-vs-normal comparisons.
  • Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because fewer than ten samples limit cohort confidence.
  • 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

Normalized Fields

18 fields

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 GSM1955436 Patients with crohn's disease 1 Human CD, 30 min Age: 25; Gender: F; Tissue: Blood Case marker detected.
Crohn's disease Case GSM1955437 Patients with crohn's disease 2 Human CD, 30 min Age: 33; Gender: M; Tissue: Blood Case marker detected.
Crohn's disease Case GSM1955438 Patients with crohn's disease 3 Human CD, 30 min Age: 47; Gender: M; Tissue: Blood Case marker detected.
Control Control GSM1955439 Healthy subjects as control 1 Control sample, 30min Age: 37; Gender: M; Tissue: Blood Sample-local control marker detected.
Control Control GSM1955440 Healthy subjects as control 2 Control sample, 30min Age: 32; Gender: F; Tissue: Blood Sample-local control marker detected.
Control Control GSM1955441 Healthy subjects as control 3 Control sample, 30min Age: 29; Gender: M; Tissue: Blood 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.