Early and long-standing rheumatoid arthritis: molecular signatures identified by gene expression profiling in synovium

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

24 case / 21 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: 45 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: Lequerre T, Bansard C, Vittecoq O, Derambure C, Hiron M, Daveau M, Tron F, Dougados M, Biga N, Auquit-Auckbur I, Milliez PY, Chiocchia G, Le X, Salier JP
Contact name: Jean Philippe SALIER
Submission date: 2008-10-02
Last update: 2012-03-20
Organization: Faculty of Medicine and Pharmacy
Department: Inserm Unit 519
Public date: 2008-10-03
Experiment types: Expression profiling by array
Platforms: GPL5215 INSERM Homo sapiens 14K array Liverpool3
Series type: Series
SubSeries: Not available
BioProject: PRJNA112571

Summary

At a given time, rheumatoid arthritis (RA) is a heterogeneous disease and its underlying molecular mechanisms is still poorly understood. Because previous microarrays studies have only focused on late RA stages, we aimed to compare the biological and molecular profiles in early and long-standing (LS) RA. Synovial biopsies obtained by arthroscopy were performed in 4 early untreated RA patients, 4 LS treated RA patients and 7 control patients. Extracted mRNA were linearly amplified and used for large-scale gene expression profiling by cDNA arrays. By gene ontology analysis, the different gene combinations obtained by comparison of early, LS RA and normal synovium were used to identify the biological processes, molecular functions and pathways involved at each stage. Three combinations of 719, 116 and 52 transcripts dissociated respectively early from LS RA patients, early or LS RA from normal synovium. We identified several gene clusters and distinct molecular signatures specifically related to early or LS RA suggesting the involvement of different pathological mechanisms at each stage. Early and LS RA have distinct molecular signatures with the participation of different biological processes during the course of the disease. These results suggest that a better knowledge of the main biological processes involved at a given RA stage might help the rheumatologist to choose the more appropriate treatment.

Overall design

PBMC then RNA were extracted from synovial biopsies of 4 eraly RA patients, 4 long-standing RA patients and from 7 normal synovium used as control. Each sample was hybridized three times in different nylon membrane.

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 45 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 Early and long-standing rheumatoid arthritis: distinct molecular signatures identified by gene-expression profiling in synovia. Arthritis research & therapy, 2009 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: 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 24 samples
Likely control group Control 21 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 1 publication; 1 DOI available: PMID 19563633.
Publication context: Early and long-standing rheumatoid arthritis: distinct molecular signatures identified by gene-expression profiling in synovia.. Arthritis research & therapy, 2009. PMID 19563633. DOI 10.1186/ar2744.

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.
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.
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

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.
Patient-tissue tumor-normal intent requires tissue or biopsy source clarity.

Normalized Fields

29 fields

Field Value Source Derived by Confidence Evidence Reason

assay_type microarray GSE13026 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence microarray dataset_accession: GSE13026 dataset_title: Early and long-standing rheumatoid arthritis: molecular signatures identified by gene expression profiling in synovium organism: Homo ... keyword match keyword match: microarray

disease rheumatoid arthritis GSE13026 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis dataset_accession: GSE13026 dataset_title: Early and long-standing rheumatoid arthritis: molecular signatures identified by gene expression profiling in synovium organism: Homo ... controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM326301 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Early RA patient 1 - hybridization 1 Rheumatoid Arthritis patient 32 years old woman controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM326302 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Early RA patient 1 - hybridization 2 Rheumatoid Arthritis patient 32 years old woman controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM326303 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Early RA patient 1 - hybridization 3 Rheumatoid Arthritis patient 32 years old woman controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM326304 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Early RA patient 2 - hybridization 1 Rheumatoid Arthritis patient 26 years old woman controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM326305 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Early RA patient 2 - hybridization 2 Rheumatoid Arthritis patient 26 years old woman controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM326306 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Early RA patient 2 - hybridization 3 Rheumatoid Arthritis patient 26 years old woman controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM326307 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Early RA patient 3 - hybridization 1 Rheumatoid Arthritis patient 29 years old man controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM326308 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Early RA patient 3 - hybridization 2 Rheumatoid Arthritis patient 29 years old man controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM326309 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Early RA patient 3 - hybridization 3 Rheumatoid Arthritis patient 29 years old man controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM326310 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Early RA patient 4 - hybridization 1 Rheumatoid Arthritis patient 40 years old man controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM326311 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Early RA patient 4 - hybridization 2 Rheumatoid Arthritis patient 40 years old man controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM326312 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Early RA patient 4 - hybridization 3 Rheumatoid Arthritis patient 40 years old man controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM326313 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Long-standing RA patient 1 - hybridization 1 Rheumatoid Arthritis patient 42 years old woman controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM326314 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Long-standing RA patient 1 - hybridization 2 Rheumatoid Arthritis patient 42 years old woman controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM326315 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Long-standing RA patient 1 - hybridization 3 Rheumatoid Arthritis patient 42 years old woman controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM326316 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Long-standing RA patient 2 - hybridization 1 Rheumatoid Arthritis patient 45 years old woman controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM326317 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Long-standing RA patient 2 - hybridization 2 Rheumatoid Arthritis patient 45 years old woman controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM326318 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Long-standing RA patient 2 - hybridization 3 Rheumatoid Arthritis patient 45 years old woman controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM326319 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Long-standing RA patient 3 - hybridization 1 Rheumatoid Arthritis patient 42 years old woman controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM326320 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Long-standing RA patient 3 - hybridization 2 Rheumatoid Arthritis patient 42 years old woman controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM326321 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Long-standing RA patient 3 - hybridization 3 Rheumatoid Arthritis patient 42 years old woman controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM326322 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Long-standing RA patient 4 - hybridization 1 Rheumatoid Arthritis patient 64 years old woman controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM326323 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Long-standing RA patient 4 - hybridization 2 Rheumatoid Arthritis patient 64 years old woman controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM326324 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis Long-standing RA patient 4 - hybridization 3 Rheumatoid Arthritis patient 64 years old woman controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

organism Homo sapiens GSE13026 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE13026 dataset_title: Early and long-standing rheumatoid arthritis: molecular signatures identified by gene expression profiling in synovium organism: Homo ... keyword match keyword match: homo sapiens

tissue blood GSE13026 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc dataset_accession: GSE13026 dataset_title: Early and long-standing rheumatoid arthritis: molecular signatures identified by gene expression profiling in synovium organism: Homo ... controlled vocabulary controlled vocabulary tissue match: pbmc

tissue synovium GSE13026 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence synovium dataset_accession: GSE13026 dataset_title: Early and long-standing rheumatoid arthritis: molecular signatures identified by gene expression profiling in synovium organism: Homo ... controlled vocabulary controlled vocabulary tissue match: synovium

Sample Group Preview

45 rows shown Show Hide

Study totals: Case 24 | Control 21 | Unassigned 0 | Excluded 0 | Ambiguous 0 45 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Rheumatoid arthritis	Case	GSM326301	Early RA patient 1 - hybridization 1	Rheumatoid Arthritis patient 32 years old woman	Case marker detected.
Rheumatoid arthritis	Case	GSM326302	Early RA patient 1 - hybridization 2	Rheumatoid Arthritis patient 32 years old woman	Case marker detected.
Rheumatoid arthritis	Case	GSM326303	Early RA patient 1 - hybridization 3	Rheumatoid Arthritis patient 32 years old woman	Case marker detected.
Rheumatoid arthritis	Case	GSM326304	Early RA patient 2 - hybridization 1	Rheumatoid Arthritis patient 26 years old woman	Case marker detected.
Rheumatoid arthritis	Case	GSM326305	Early RA patient 2 - hybridization 2	Rheumatoid Arthritis patient 26 years old woman	Case marker detected.
Rheumatoid arthritis	Case	GSM326306	Early RA patient 2 - hybridization 3	Rheumatoid Arthritis patient 26 years old woman	Case marker detected.
Rheumatoid arthritis	Case	GSM326307	Early RA patient 3 - hybridization 1	Rheumatoid Arthritis patient 29 years old man	Case marker detected.
Rheumatoid arthritis	Case	GSM326308	Early RA patient 3 - hybridization 2	Rheumatoid Arthritis patient 29 years old man	Case marker detected.
Rheumatoid arthritis	Case	GSM326309	Early RA patient 3 - hybridization 3	Rheumatoid Arthritis patient 29 years old man	Case marker detected.
Rheumatoid arthritis	Case	GSM326310	Early RA patient 4 - hybridization 1	Rheumatoid Arthritis patient 40 years old man	Case marker detected.
Rheumatoid arthritis	Case	GSM326311	Early RA patient 4 - hybridization 2	Rheumatoid Arthritis patient 40 years old man	Case marker detected.
Rheumatoid arthritis	Case	GSM326312	Early RA patient 4 - hybridization 3	Rheumatoid Arthritis patient 40 years old man	Case marker detected.
Rheumatoid arthritis	Case	GSM326313	Long-standing RA patient 1 - hybridization 1	Rheumatoid Arthritis patient 42 years old woman	Case marker detected.
Rheumatoid arthritis	Case	GSM326314	Long-standing RA patient 1 - hybridization 2	Rheumatoid Arthritis patient 42 years old woman	Case marker detected.
Rheumatoid arthritis	Case	GSM326315	Long-standing RA patient 1 - hybridization 3	Rheumatoid Arthritis patient 42 years old woman	Case marker detected.
Rheumatoid arthritis	Case	GSM326316	Long-standing RA patient 2 - hybridization 1	Rheumatoid Arthritis patient 45 years old woman	Case marker detected.
Rheumatoid arthritis	Case	GSM326317	Long-standing RA patient 2 - hybridization 2	Rheumatoid Arthritis patient 45 years old woman	Case marker detected.
Rheumatoid arthritis	Case	GSM326318	Long-standing RA patient 2 - hybridization 3	Rheumatoid Arthritis patient 45 years old woman	Case marker detected.
Rheumatoid arthritis	Case	GSM326319	Long-standing RA patient 3 - hybridization 1	Rheumatoid Arthritis patient 42 years old woman	Case marker detected.
Rheumatoid arthritis	Case	GSM326320	Long-standing RA patient 3 - hybridization 2	Rheumatoid Arthritis patient 42 years old woman	Case marker detected.
Rheumatoid arthritis	Case	GSM326321	Long-standing RA patient 3 - hybridization 3	Rheumatoid Arthritis patient 42 years old woman	Case marker detected.
Rheumatoid arthritis	Case	GSM326322	Long-standing RA patient 4 - hybridization 1	Rheumatoid Arthritis patient 64 years old woman	Case marker detected.
Rheumatoid arthritis	Case	GSM326323	Long-standing RA patient 4 - hybridization 2	Rheumatoid Arthritis patient 64 years old woman	Case marker detected.
Rheumatoid arthritis	Case	GSM326324	Long-standing RA patient 4 - hybridization 3	Rheumatoid Arthritis patient 64 years old woman	Case marker detected.
Control	Control	GSM326325	Control patient 1 - hybridization 1	Control 22 years old woman	Sample-local control marker detected.
Control	Control	GSM326326	Control patient 1 - hybridization 2	Control 22 years old woman	Sample-local control marker detected.
Control	Control	GSM326327	Control patient 1 - hybridization 3	Control 22 years old woman	Sample-local control marker detected.
Control	Control	GSM326328	Control patient 2 - hybridization 1	Control 26 years old man	Sample-local control marker detected.
Control	Control	GSM326329	Control patient 2 - hybridization 2	Control 26 years old man	Sample-local control marker detected.
Control	Control	GSM326330	Control patient 2 - hybridization 3	Control 26 years old man	Sample-local control marker detected.
Control	Control	GSM326331	Control patient 3 - hybridization 1	Control 25 years old man	Sample-local control marker detected.
Control	Control	GSM326332	Control patient 3 - hybridization 2	Control 25 years old man	Sample-local control marker detected.
Control	Control	GSM326333	Control patient 3 - hybridization 3	Control 25 years old man	Sample-local control marker detected.
Control	Control	GSM326334	Control patient 4 - hybridization 1	Control 33 years old woman	Sample-local control marker detected.
Control	Control	GSM326335	Control patient 4 - hybridization 2	Control 33 years old woman	Sample-local control marker detected.
Control	Control	GSM326336	Control patient 4 - hybridization 3	Control 33 years old woman	Sample-local control marker detected.
Control	Control	GSM326337	Control patient 5 - hybridization 1	Control Age unknown, man	Sample-local control marker detected.
Control	Control	GSM326338	Control patient 5 - hybridization 2	Control Age unknown, man	Sample-local control marker detected.
Control	Control	GSM326339	Control patient 5 - hybridization 3	Control Age unknown, man	Sample-local control marker detected.
Control	Control	GSM326340	Control patient 6 - hybridization 1	Control 27 years old man	Sample-local control marker detected.
Control	Control	GSM326341	Control patient 6 - hybridization 2	Control 27 years old man	Sample-local control marker detected.
Control	Control	GSM326342	Control patient 6 - hybridization 3	Control 27 years old man	Sample-local control marker detected.
Control	Control	GSM326343	Control patient 7 - hybridization 1	Control 29 years old man	Sample-local control marker detected.
Control	Control	GSM326344	Control patient 7 - hybridization 2	Control 29 years old man	Sample-local control marker detected.
Control	Control	GSM326345	Control patient 7 - hybridization 3	Control 29 years old man	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