GSE197057

Expression data (U133 Plus 2.0) from fibroblast like synoviocytes from patients with rheumatoid arthritis (RA-FLS) stimulated by LIGHT.

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
Treatment vs control Design classification does not establish patient pairs.
Comparison type
Tumor vs normal
Contributors
Fukuda K, Miura Y, Maeda T, Kikuchi K, Takashima Y, Hayashi S, Matsumoto T, Kuroda R
Contact name
Koji Fukuda
Submission date
2022-02-19
Last update
2024-03-07
Organization
Kobe University Graduate School of Medicine
Department
Department of Orthopaedic Surgery
Public date
2022-02-20
Experiment types
Expression profiling by array
Platforms
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
Series type
Series
SubSeries
Not available
BioProject
PRJNA808619

Summary

LIGHT/TNFSF6, a member of the tumor necrosis factor (TNF) superfamily, can promote apoptosis in activated primary B cells, T cells, dendritic cells, and synovial fibroblasts through Fas and is involved in the pathogenesis of autoimmune diseases including rheumatoid arthritis (RA). Meanwhile, decoy receptor 3 (DcR3) competitively binds soluble LIGHT in addition to TL1A and FasL and inhibits the signaling of LIGHT via HEVN and. Therefore, LIGHT-DcR3/HEVN/ signaling may be involved in the pathogenesis of RA. We hypothesized that LIGHT regulates the gene expression in RA-FLS. We used to search for genes in which expression in RA-FLS is regulated by LIGHT.

Overall design

RA-FLS were obtained from 4 RA patients (sample1-4). Each sample was incubated with either 1.0 μg/ml recombinant human LIGHT protein or phosphate buffered saline diluted with serum-free Opti-MEM medium as non-stimulated control. Gene expression in RA-FLS stimulated by LIGHT was compared with that of their respective non-stimulated controls.

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.

1 linked publication 1 DOI

Primary publication

  1. LIGHT regulated gene expression in rheumatoid synovial fibroblasts. Molecular biology reports, 2024
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: Treatment status metadata normalized where treatment is part of the comparison. 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
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

  • 4 samples need manual grouping review.

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

4 review-needed samples and 0 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 were flagged for manual review.

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 Control 4 samples

Intent Interpretation

  • Downgrade or exclusion reason Comparison: Treatment 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 1 publication; 1 DOI available: PMID 38401037.
  • Publication context: LIGHT regulated gene expression in rheumatoid synovial fibroblasts.. Molecular biology reports, 2024. PMID 38401037. DOI 10.1007/s11033-024-09311-0.

Cautions

  • Comparison: Treatment vs control. Specimen: Unclear specimen/source. Comparison suitability: 0%.
  • Downgraded for tissue search because it is a treatment/control experiment.
  • Downgraded for tissue search because study design or specimen source is unclear.
  • Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
  • Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons.
  • 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 - Treatment 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

16 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 GSM5907682 RA-FLS_sample 1_LIGHT-stimulated Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample1, LIGHT-stimulated Cell type: Fibroblast like synoviocytes; Patient diagnosis: Rheumatoid arthritis; Stimulation: LIGHT-stimulated treated sample: Treated sample may need exclusion outside treatment comparisons.
Rheumatoid arthritis Case GSM5907684 RA-FLS_sample 2_LIGHT-stimulated Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample2, LIGHT-stimulated Cell type: Fibroblast like synoviocytes; Patient diagnosis: Rheumatoid arthritis; Stimulation: LIGHT-stimulated treated sample: Treated sample may need exclusion outside treatment comparisons.
Rheumatoid arthritis Case GSM5907686 RA-FLS_sample 3_LIGHT-stimulated Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample3, LIGHT-stimulated Cell type: Fibroblast like synoviocytes; Patient diagnosis: Rheumatoid arthritis; Stimulation: LIGHT-stimulated treated sample: Treated sample may need exclusion outside treatment comparisons.
Rheumatoid arthritis Case GSM5907688 RA-FLS_sample 4_LIGHT-stimulated Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample4, LIGHT-stimulated Cell type: Fibroblast like synoviocytes; Patient diagnosis: Rheumatoid arthritis; Stimulation: LIGHT-stimulated treated sample: Treated sample may need exclusion outside treatment comparisons.
Control Control GSM5907681 RA-FLS_sample 1_control Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample1 Cell type: Fibroblast like synoviocytes; Patient diagnosis: Rheumatoid arthritis; Stimulation: Control Sample-local control marker detected.
Control Control GSM5907683 RA-FLS_sample 2_control Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample2 Cell type: Fibroblast like synoviocytes; Patient diagnosis: Rheumatoid arthritis; Stimulation: Control Sample-local control marker detected.
Control Control GSM5907685 RA-FLS_sample 3_control Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample3 Cell type: Fibroblast like synoviocytes; Patient diagnosis: Rheumatoid arthritis; Stimulation: Control Sample-local control marker detected.
Control Control GSM5907687 RA-FLS_sample 4_control Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample4 Cell type: Fibroblast like synoviocytes; Patient diagnosis: Rheumatoid arthritis; Stimulation: Control 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.