GSE1402

Juvenile Rheumatoid Arthritis Profiles In PBMC and SFMC

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

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.

Summary

Biotinylated cRNA was synthesized from total RNA (Enzo; Farmingdale, NY) and processed according to the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix; Santa Clara, CA). 57 samples: 5 pauciarticular PBMC, 15 polyarticular PBMC, 11 control PMBC, 6 JSpA PBMC, 5 pauciarticular SFMC, 10 polyarticular PBMC, 5 JSpA SFMC classified by course. Keywords = juvenile rheumatoid arthritis (JRA) Keywords = peripheral blood mononuclear cells (PBMC) Keywords = synovial fluid mononuclear cells (SFMC) Keywords: other

Overall design

Source Evidence

4 sources
Source Contribution Status
GEO

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

Sample records
57 GSM samples
Primary source
recount3

Planned trusted source for processed count availability.

No match found
Expression Atlas

Curated expression experiment linkage and source URL.

Expression Atlas accession
E-GEOD-1402
Available
PubMed

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

3 linked publications 3 DOIs

Primary publication

  1. Gene expression in juvenile arthritis and spondyloarthropathy: pro-angiogenic ELR+ chemokine genes relate to course of arthritis. Rheumatology (Oxford, England), 2004

Related publications

  1. Identification and validation of susceptibility modules and hub genes in polyarticular juvenile idiopathic arthritis using WGCNA and machine learning. Autoimmunity, 2025
  2. A Cross-Tissue Transcriptome-Wide Association Study Identifies Novel Susceptibility Genes for Juvenile Idiopathic Arthritis in Asia and Europe. Frontiers in immunology, 2022
Available

Metadata Quality Components

Analysis Readiness

Review before analysis
85% 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

3/15 pts

Unassigned or review-needed samples remain before analysis.

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

  • 11 samples are still unassigned.

Next Steps

  • Resolve unassigned or review-needed samples in the grouping table.

Analysis Preparation Checklist

4/6 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

Needs review

0 review-needed samples and 11 unassigned samples remain.

Resolve ambiguous and unassigned samples before finalizing the contrast.

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.

One or more samples are unassigned and need manual grouping decisions.

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 35 samples
  • Likely control group Control 11 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: Rheumatoid arthritis.
  • Processed data is available for downstream review.
  • External evidence: Expression Atlas curated experiment link is available.
  • External evidence: PubMed links 3 publications; 3 DOIs available: PMID 15150433, PMID 35967305, PMID 39699225.
  • Publication context: Gene expression in juvenile arthritis and spondyloarthropathy: pro-angiogenic ELR+ chemokine genes relate to course of arthritis.. Rheumatology (Oxford, England), 2004. PMID 15150433. DOI 10.1093/rheumatology/keh224.
  • Publication context: A Cross-Tissue Transcriptome-Wide Association Study Identifies Novel Susceptibility Genes for Juvenile Idiopathic Arthritis in Asia and Europe.. Frontiers in immunology, 2022. PMID 35967305. DOI 10.3389/fimmu.2022.941398.
  • Publication context: Identification and validation of susceptibility modules and hub genes in polyarticular juvenile idiopathic arthritis using WGCNA and machine learning.. Autoimmunity, 2025. PMID 39699225. DOI 10.1080/08916934.2024.2437239.

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 microarray cohorts should be compared separately from RNA-seq cohorts.
  • Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

Normalized Fields

382 fields

Sample Group Preview

57 rows shown
Show Hide
Study totals: Case 35 | Control 11 | Unassigned 11 | Excluded 0 | Ambiguous 0 57 rows shown
Group Role Accession Title Source / characteristics Reason
Rheumatoid arthritis Case GSM23159 8003PBMC PBMC None Case marker detected.
Rheumatoid arthritis Case GSM23160 817PBMC PBMC None Case marker detected.
Rheumatoid arthritis Case GSM23161 9161PBMC PBMC None Case marker detected.
Rheumatoid arthritis Case GSM23162 9264PBMC PBMC None Case marker detected.
Rheumatoid arthritis Case GSM23163 976PBMC PBMC None Case marker detected.
Rheumatoid arthritis Case GSM23164 1073PBMC PBMC None Case marker detected.
Rheumatoid arthritis Case GSM23165 1081PBMC PBMC None Case marker detected.
Rheumatoid arthritis Case GSM23166 1087PBMC PBMC None Case marker detected.
Rheumatoid arthritis Case GSM23167 19PBMC PBMC None Case marker detected.
Rheumatoid arthritis Case GSM23168 801PBMC PBMC None Case marker detected.
Rheumatoid arthritis Case GSM23169 824PBMC PBMC None Case marker detected.
Rheumatoid arthritis Case GSM23170 831PBMC PBMC None Case marker detected.
Rheumatoid arthritis Case GSM23171 850PBMC PBMC None Case marker detected.
Rheumatoid arthritis Case GSM23172 872PBMC PBMC None Case marker detected.
Rheumatoid arthritis Case GSM23173 878PBMC PBMC None Case marker detected.
Rheumatoid arthritis Case GSM23174 894PBMC PBMC None Case marker detected.
Rheumatoid arthritis Case GSM23175 912PBMC PBMC None Case marker detected.
Rheumatoid arthritis Case GSM23176 9137PBMC PBMC None Case marker detected.
Rheumatoid arthritis Case GSM23177 9272PBMC PBMC None Case marker detected.
Rheumatoid arthritis Case GSM23178 993PBMC PBMC None Case marker detected.
Rheumatoid arthritis Case GSM23196 8003SFMC SFMC None Case marker detected.
Rheumatoid arthritis Case GSM23197 817SFMC SFMC None Case marker detected.
Rheumatoid arthritis Case GSM23198 9161SFMC SFMC None Case marker detected.
Rheumatoid arthritis Case GSM23199 9264SFMC SFMC None Case marker detected.
Rheumatoid arthritis Case GSM23200 976SFMC SFMC None Case marker detected.
Rheumatoid arthritis Case GSM23201 1073SFMC SFMC None Case marker detected.
Rheumatoid arthritis Case GSM23202 1087PBSFMC SFMC None Case marker detected.
Rheumatoid arthritis Case GSM23203 824SFMC SFMC None Case marker detected.
Rheumatoid arthritis Case GSM23204 831SFMC SFMC None Case marker detected.
Rheumatoid arthritis Case GSM23205 850SFMC SFMC None Case marker detected.
Rheumatoid arthritis Case GSM23206 872SFMC SFMC None Case marker detected.
Rheumatoid arthritis Case GSM23207 878SFMC SFMC None Case marker detected.
Rheumatoid arthritis Case GSM23208 9137SFMC SFMC None Case marker detected.
Rheumatoid arthritis Case GSM23209 9272SFMC SFMC None Case marker detected.
Rheumatoid arthritis Case GSM23210 993SFMC SFMC None Case marker detected.
Control Control GSM23185 1082PBMC PBMC None Sample-local control marker detected.
Control Control GSM23186 1083PBMC PBMC None Sample-local control marker detected.
Control Control GSM23187 1085PBMC PBMC None Sample-local control marker detected.
Control Control GSM23188 1087CTRPBMC PBMC None Sample-local control marker detected.
Control Control GSM23189 1089PBMC PBMC None Sample-local control marker detected.
Control Control GSM23190 1095PBMC PBMC None Sample-local control marker detected.
Control Control GSM23191 7021.31PBMC PBMC None Sample-local control marker detected.
Control Control GSM23192 7113.3PBMC PBMC None Sample-local control marker detected.
Control Control GSM23193 7118.3PBMC PBMC None Sample-local control marker detected.
Control Control GSM23194 7149.3PBMC PBMC None Sample-local control marker detected.
Control Control GSM23195 813.3PBMC PBMC None Sample-local control marker detected.
Unassigned Unassigned GSM23179 18042PBMC PBMC None No explicit case or control marker detected.
Unassigned Unassigned GSM23180 18057PBMC PBMC None No explicit case or control marker detected.
Unassigned Unassigned GSM23181 7177PBMC PBMC None No explicit case or control marker detected.
Unassigned Unassigned GSM23182 845PBMC PBMC None No explicit case or control marker detected.
Unassigned Unassigned GSM23183 9150PBMC PBMC None No explicit case or control marker detected.
Unassigned Unassigned GSM23184 9245PBMC PBMC None No explicit case or control marker detected.
Unassigned Unassigned GSM23211 18042SFMC SFMC None No explicit case or control marker detected.
Unassigned Unassigned GSM23212 18057SFMC SFMC None No explicit case or control marker detected.
Unassigned Unassigned GSM23213 7177SFMC SFMC None No explicit case or control marker detected.
Unassigned Unassigned GSM23214 845SFMC SFMC None No explicit case or control marker detected.
Unassigned Unassigned GSM23215 9245SFMC SFMC None No explicit case or 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.