GSE153378

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

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: Tissue
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, Hayashi S, Matsumoto T, Kuroda R
Contact name: Koji Fukuda
Submission date: 2020-06-26
Last update: 2021-08-11
Organization: Kobe University Graduate School of Medicine
Department: Department of Orthopaedic Surgery
Public date: 2020-06-30
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: PRJNA642862

Summary

Fas ligand (FasL)/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 FasL in addition to TL1A and LIGHT and inhibits the signaling of FasL via Fas. Therefore, FasL-DcR3/Fas signaling may be involved in the pathogenesis of RA. We hypothesized that FasL regulates the gene expression in RA-FLS. We used to search for genes in which expression in RA-FLS is regulated by FasL.

Overall design

RA-FLS were obtained from 4 RA patients (sample1-4). Each sample was incubated with either 1.0 μg/ml recombinant human FasL protein or phosphate buffered saline diluted with serum-free Opti-MEM medium as non-stimulated control. Gene expression in RA-FLS stimulated by FasL 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 Expression profiling of genes in rheumatoid fibroblast-like synoviocytes regulated by Fas ligand via cDNA microarray analysis. Experimental and therapeutic medicine, 2021 PubMed DOI	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 Downgraded for tissue search because it is a treatment/control experiment. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

Comparison: Treatment vs control. Specimen: Tissue. Comparison suitability: 0%.
Interpreted disease metadata: Rheumatoid arthritis.
Processed data is available for downstream review.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 34345282.
Publication context: Expression profiling of genes in rheumatoid fibroblast-like synoviocytes regulated by Fas ligand via cDNA microarray analysis.. Experimental and therapeutic medicine, 2021. PMID 34345282. DOI 10.3892/etm.2021.10432.

Cautions

Downgraded for tissue search because it is a treatment/control experiment.
Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons.
Overall score capped because comparison suitability is weak for the selected search intent.
Overall score capped because fewer than ten samples limit cohort confidence.
Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

Treated samples may need review depending on the comparison.
Microarray expression context was detected; compare separately from RNA-seq cohorts.
Microarray datasets are downgraded in the patient-tissue tumor-normal intent unless secondary assays are explicitly enabled.

Normalized Fields

16 fields

Field Value Source Derived by Confidence Evidence Reason

assay_type microarray GSE153378 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence microarray dataset_accession: GSE153378 dataset_title: Expression data (U133 Plus 2.0) from fibroblast like synoviocytes from patients with rheumatoid arthritis (RA-FLS) stimulated by FasL... keyword match keyword match: microarray

disease rheumatoid arthritis GSE153378 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis dataset_accession: GSE153378 dataset_title: Expression data (U133 Plus 2.0) from fibroblast like synoviocytes from patients with rheumatoid arthritis (RA-FLS) stimulated by FasL... controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4643211 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis RA-FLS_sample1_control_for_FasL Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample1 tissue: Fibroblast like synoviocytes controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4643212 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis RA-FLS_sample1_FasL-stimulated Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample1, FasL-stimulated tissue: Fibroblast like synoviocytes controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4643213 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis RA-FLS_sample2_control_for_FasL Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample2 tissue: Fibroblast like synoviocytes controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4643214 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis RA-FLS_sample2_FasL-stimulated Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample2, FasL-stimulated tissue: Fibroblast like synoviocytes controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4643215 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis RA-FLS_sample3_control_for_FasL Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample3 tissue: Fibroblast like synoviocytes controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4643216 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis RA-FLS_sample3_FasL-stimulated Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample3, FasL-stimulated tissue: Fibroblast like synoviocytes controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4643217 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis RA-FLS_sample4_control_for_FasL Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample4 tissue: Fibroblast like synoviocytes controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM4643218 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis RA-FLS_sample4_FasL-stimulated Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample4, FasL-stimulated tissue: Fibroblast like synoviocytes controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

organism Homo sapiens GSE153378 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE153378 dataset_title: Expression data (U133 Plus 2.0) from fibroblast like synoviocytes from patients with rheumatoid arthritis (RA-FLS) stimulated by FasL... keyword match keyword match: homo sapiens

tissue synovium GSE153378 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence synovial dataset_accession: GSE153378 dataset_title: Expression data (U133 Plus 2.0) from fibroblast like synoviocytes from patients with rheumatoid arthritis (RA-FLS) stimulated by FasL... controlled vocabulary controlled vocabulary tissue match: synovial

treatment_status treated GSM4643212 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence stimulated RA-FLS_sample1_FasL-stimulated Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample1, FasL-stimulated tissue: Fibroblast like synoviocytes controlled vocabulary controlled vocabulary treatment status match: stimulated

treatment_status treated GSM4643214 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence stimulated RA-FLS_sample2_FasL-stimulated Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample2, FasL-stimulated tissue: Fibroblast like synoviocytes controlled vocabulary controlled vocabulary treatment status match: stimulated

treatment_status treated GSM4643216 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence stimulated RA-FLS_sample3_FasL-stimulated Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample3, FasL-stimulated tissue: Fibroblast like synoviocytes controlled vocabulary controlled vocabulary treatment status match: stimulated

treatment_status treated GSM4643218 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence stimulated RA-FLS_sample4_FasL-stimulated Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample4, FasL-stimulated tissue: Fibroblast like synoviocytes controlled vocabulary controlled vocabulary treatment status match: stimulated

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	GSM4643212	RA-FLS_sample1_FasL-stimulated	Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample1, FasL-stimulated Tissue: Fibroblast like synoviocytes	treated sample: Treated sample may need exclusion outside treatment comparisons.
Rheumatoid arthritis	Case	GSM4643214	RA-FLS_sample2_FasL-stimulated	Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample2, FasL-stimulated Tissue: Fibroblast like synoviocytes	treated sample: Treated sample may need exclusion outside treatment comparisons.
Rheumatoid arthritis	Case	GSM4643216	RA-FLS_sample3_FasL-stimulated	Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample3, FasL-stimulated Tissue: Fibroblast like synoviocytes	treated sample: Treated sample may need exclusion outside treatment comparisons.
Rheumatoid arthritis	Case	GSM4643218	RA-FLS_sample4_FasL-stimulated	Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample4, FasL-stimulated Tissue: Fibroblast like synoviocytes	treated sample: Treated sample may need exclusion outside treatment comparisons.
Control	Control	GSM4643211	RA-FLS_sample1_control_for_FasL	Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample1 Tissue: Fibroblast like synoviocytes	Sample-local control marker detected.
Control	Control	GSM4643213	RA-FLS_sample2_control_for_FasL	Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample2 Tissue: Fibroblast like synoviocytes	Sample-local control marker detected.
Control	Control	GSM4643215	RA-FLS_sample3_control_for_FasL	Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample3 Tissue: Fibroblast like synoviocytes	Sample-local control marker detected.
Control	Control	GSM4643217	RA-FLS_sample4_control_for_FasL	Fibroblast like synoviocytes from patient with rheumatoid arthritis, sample4 Tissue: Fibroblast like synoviocytes	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.

Summary

Overall design

Source Evidence

Primary publication

Metadata Quality Components

Analysis Readiness

Blockers

Next Steps

Analysis Preparation Checklist

Bioinformatician Review

Why This Is Ranked Here

Applied Review Decisions

Derived Classifications

Intent Interpretation

Ranking Facts

Supporting evidence

Cautions

Dataset Warnings

Normalized Fields

Sample Group Preview

Use as Discovery Cohort