GSE2053

RAvs.ND

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

4 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
8 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
Ungethuem U, Witt H
Contact name
Ute Ungethuem
Submission date
2004-12-09
Last update
2012-03-16
Organization
Charité University Hospital
Department
Core Center for Functional Genome Research
Public date
2004-12-10
Experiment types
Expression profiling by array
Platforms
GPL1740 HUMAN UNIGENE SetI Part 1
Series type
Series
SubSeries
Not available
BioProject
PRJNA91713

Summary

Rheumatoid arthritis (RA) is a chronic, inflammatory joint disease of unknown etiology and pronounced inter-patient heterogeneity. To characterize RA at the molecular level and to uncover key pathomechanisms, we performed whole-genome gene expression analyses. Synovial tissues from rheumatoid arthritis patients were compared to those from to normal donors. Keywords: repeat sample

Overall design

Rheumatoid in comparison to normal donors were investigated. For both groups samples derived from individual patients and or pools of patients were hybridised.

Source Evidence

4 sources
Source Contribution Status
GEO

Original dataset metadata, sample metadata, source links, and GEO data availability flags.

Sample records
8 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.

3 linked publications 3 DOIs

Primary publication

  1. Molecular signatures and new candidates to target the pathogenesis of rheumatoid arthritis. Physiological genomics, 2010

Related publications

  1. Bioinformatic analysis to find small molecules related to rheumatoid arthritis. International journal of rheumatic diseases, 2014
  2. KIF11 promotes rheumatoid arthritis pathogenesis by activating M1 macrophage polarization and promoting inflammatory cytokine secretion. PloS one, 2026
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

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 Rheumatoid arthritis Disease context came from Normalization rules.
  • Likely case group Rheumatoid arthritis 4 samples
  • Likely control group Normal tissue 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: Rheumatoid arthritis.
  • Processed data is available for downstream review.
  • External evidence: PubMed links 3 publications; 3 DOIs available: PMID 20858714, PMID 24238402, PMID 42127012.
  • Publication context: Molecular signatures and new candidates to target the pathogenesis of rheumatoid arthritis.. Physiological genomics, 2010. PMID 20858714. DOI 10.1152/physiolgenomics.00004.2010.
  • Publication context: Bioinformatic analysis to find small molecules related to rheumatoid arthritis.. International journal of rheumatic diseases, 2014. PMID 24238402. DOI 10.1111/1756-185X.12201.
  • Publication context: KIF11 promotes rheumatoid arthritis pathogenesis by activating M1 macrophage polarization and promoting inflammatory cytokine secretion.. PloS one, 2026. PMID 42127012. DOI 10.1371/journal.pone.0347313.

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.
  • Overall score capped because comparison suitability is weak for the selected search intent.
  • Overall score capped because fewer than ten samples limit cohort confidence.
  • 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

12 fields

Sample Group Preview

8 rows shown Show Hide
Study totals: Case 4 | Control 4 | Unassigned 0 | Excluded 0 | Ambiguous 0 8 rows shown
Group Role Accession Title Source / characteristics Reason
Rheumatoid arthritis Case GSM37434 RA_C Rheumatoid arthritis Age: 45; Gender: Female Case marker detected.
Rheumatoid arthritis Case GSM37435 RA_D Rheumatoid arthritis Age: 41; Gender: Male; Sample 2; Age: 66; Gender: Female Case marker detected.
Rheumatoid arthritis Case GSM37436 RA_E Rheumatoid arthritis Age: 65; Gender: Female Case marker detected.
Rheumatoid arthritis Case GSM37437 RA_F Rheumatoid arthritis Age: 45; Gender: Female; Sample 2; Age: 46; Gender: Female; Age: 64; Gender: Male Case marker detected.
Normal tissue Control GSM37430 ND_6 Normal donor Sample 1; Age: 68; Gender: Male; Sample 2; Age: 77; Gender: Female; Sample 3; Age: 72; Gender: Male; Sample 4; Age: Unknown; Gender: Unknown Control marker detected.
Normal tissue Control GSM37431 ND_7 Normal donor Sample 1; Age: 58; Gender: Male; Sample 2; Age: 58; Gender: Male Control marker detected.
Normal tissue Control GSM37432 ND_8 Normal donor Age: 58; Gender: Male; Sample 2; Age: 64; Gender: Male Control marker detected.
Normal tissue Control GSM37433 ND_9 Normal donor Age: 58; Gender: Male; Sample 2; Age: 69; Gender: Female 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.