GSE128813

The transcriptome analysis of regulatory networks in RA-FLSs

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.

Source: GEO
Assay: microarray
Organism: Homo sapiens
Whole-study samples: 6 samples
Specimen: Cell line
Reported/interpreted study design: Disease/model vs control Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Bi X, Pan Y, Xuan B
Contact name: Bi Xuan
Submission date: 2019-03-25
Last update: 2020-01-08
Organization: The Third Affiliated Hospital of Sun Yat-sen University
Department: Department of Internal Medicine,
Public date: 2020-01-08
Experiment types: Expression profiling by array; Non-coding RNA profiling by array
Platforms: GPL21827 Agilent-079487 Arraystar Human LncRNA microarray V4 (Probe Name version)
Series type: Series
SubSeries: Not available
BioProject: PRJNA528936

Summary

Rheumatoid arthritis (RA) is a common chronic inflammatory joint disease characterized by persistent synovial hyperplasia and progressive destruction of joint cartilage and bone.Fibroblast-like synoviocytes (FLSs), a prominent component of hyperplastic synovial pannus tissue, are the primary effector cells in RA synovial hyperplasia and invasion. However, the underlying molecular mechanisms remain unclear. Here, we apply transcriptome to assay the regulatory networks which contribute to the proliferation, migration and invasion of RA-FLSs .

Overall design

We investigated the differential expression profiles of mRNA and lncRNA in FLSs between two groups: the RA group (fibroblast-like synoviocytes of rheumatoid arthritis patients ), the healthy control groups (fibroblast-like synoviocytes of patients who underwent arthroscopic surgery for knee meniscus injuries or cruciate ligament rupture and had no medical history of acute or chronic joint abnormalities or systemic disease). The data of each group are collected from independent experiments in triplicate. Transcriptomic analysis was carried out using a microarray (Arraystar Human lncRNA Gene Expression Microarrays V4.0; Agilent Technology, Santa Clara, USA), which includes about 40,173 LncRNAs and 20,730 coding transcripts.

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 6 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 LncRNA PICSAR promotes cell proliferation, migration and invasion of fibroblast-like synoviocytes by sponging miRNA-4701-5p in rheumatoid arthritis. EBioMedicine, 2019 PubMed DOI Related publications Identification of serum exosomal lncRNAs and their potential regulation of characteristic genes of fibroblast-like synoviocytes in rheumatoid arthritis. International immunopharmacology, 2024 PubMed DOI Identification of the potential regulatory interactions in rheumatoid arthritis through a comprehensive analysis of lncRNA-related ceRNA networks. BMC musculoskeletal disorders, 2023 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

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

6 samples need manual grouping review.
Secondary RNA assay context should be analyzed separately from ordinary bulk RNA-seq.

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

6 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 3 samples
Likely control group Healthy control 3 samples

Intent Interpretation

Downgrade or exclusion reason Downgraded for tissue search because it is a model-system experiment. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

Comparison: Disease/model vs control. Specimen: Cell line. Comparison suitability: 0%.
Interpreted disease metadata: Rheumatoid arthritis.
Processed data is available for downstream review.
External evidence: PubMed links 3 publications; 3 DOIs available: PMID 31791845, PMID 37814309, PMID 39433011.
Publication context: LncRNA PICSAR promotes cell proliferation, migration and invasion of fibroblast-like synoviocytes by sponging miRNA-4701-5p in rheumatoid arthritis.. EBioMedicine, 2019. PMID 31791845. DOI 10.1016/j.ebiom.2019.11.024.
Publication context: Identification of the potential regulatory interactions in rheumatoid arthritis through a comprehensive analysis of lncRNA-related ceRNA networks.. BMC musculoskeletal disorders, 2023. PMID 37814309. DOI 10.1186/s12891-023-06936-3.
Publication context: Identification of serum exosomal lncRNAs and their potential regulation of characteristic genes of fibroblast-like synoviocytes in rheumatoid arthritis.. International immunopharmacology, 2024. PMID 39433011. DOI 10.1016/j.intimp.2024.113382.

Cautions

Downgraded for tissue search because it is a model-system experiment.
Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
Excluded sample type flags reduce suitability.
Disease/control design without a tumor/normal comparison is outside tumor/normal triage.
Organoid or cell-line experiment downgraded for patient tissue search intent.
Microarray expression context downgraded below primary bulk RNA-seq for the default tissue ranking.
Excluded model-system sample markers reduce suitability.
Overall score capped because comparison suitability is weak for the selected search intent.
Overall score capped because fewer than ten samples limit cohort confidence.
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

Multiple sample type labels or exclusion flags were detected.
Cell line samples appear to be included.
Secondary RNA assay context such as small RNA, miRNA, circRNA, or non-coding RNA was detected.
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

22 fields

Field Value Source Derived by Confidence Evidence Reason

assay_type microarray GSE128813 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence microarray dataset_accession: GSE128813 dataset_title: The transcriptome analysis of regulatory networks in RA-FLSs organism: Homo sapiens assay_type: microarray processed_data_available: ... keyword match keyword match: microarray

control_type healthy control GSM3685851 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control Normal1 Fibroblast-like synoviocytes of healthy control subject status: healthy control; cell type: human healthy control synoviocytes cell line controlled vocabulary controlled vocabulary control type match: healthy control

control_type healthy control GSM3685852 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control Normal2 Fibroblast-like synoviocytes of healthy control subject status: healthy control; cell type: human healthy control synoviocytes cell line controlled vocabulary controlled vocabulary control type match: healthy control

control_type healthy control GSM3685853 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control Normal3 Fibroblast-like synoviocytes of healthy control subject status: healthy control; cell type: human healthy control synoviocytes cell line controlled vocabulary controlled vocabulary control type match: healthy control

disease rheumatoid arthritis GSE128813 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis dataset_accession: GSE128813 dataset_title: The transcriptome analysis of regulatory networks in RA-FLSs organism: Homo sapiens assay_type: microarray processed_data_available: ... controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM3685848 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis LJR Fibroblast-like synoviocytes of rheumatoid arthritis subject status: rheumatoid arthritis patient; cell type: human rheumatoid arthritis synoviocytes cell line controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM3685849 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis RA3 Fibroblast-like synoviocytes of rheumatoid arthritis subject status: rheumatoid arthritis patient; cell type: human rheumatoid arthritis synoviocytes cell line controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM3685850 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis RA4 Fibroblast-like synoviocytes of rheumatoid arthritis subject status: rheumatoid arthritis patient; cell type: human rheumatoid arthritis synoviocytes cell line controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

excluded_sample_type cell line GSM3685848 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence cell line LJR Fibroblast-like synoviocytes of rheumatoid arthritis subject status: rheumatoid arthritis patient; cell type: human rheumatoid arthritis synoviocytes cell line controlled vocabulary controlled vocabulary cell line match: cell line

excluded_sample_type cell line GSM3685849 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence cell line RA3 Fibroblast-like synoviocytes of rheumatoid arthritis subject status: rheumatoid arthritis patient; cell type: human rheumatoid arthritis synoviocytes cell line controlled vocabulary controlled vocabulary cell line match: cell line

excluded_sample_type cell line GSM3685850 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence cell line RA4 Fibroblast-like synoviocytes of rheumatoid arthritis subject status: rheumatoid arthritis patient; cell type: human rheumatoid arthritis synoviocytes cell line controlled vocabulary controlled vocabulary cell line match: cell line

excluded_sample_type cell line GSM3685851 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence cell line Normal1 Fibroblast-like synoviocytes of healthy control subject status: healthy control; cell type: human healthy control synoviocytes cell line controlled vocabulary controlled vocabulary cell line match: cell line

excluded_sample_type cell line GSM3685852 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence cell line Normal2 Fibroblast-like synoviocytes of healthy control subject status: healthy control; cell type: human healthy control synoviocytes cell line controlled vocabulary controlled vocabulary cell line match: cell line

excluded_sample_type cell line GSM3685853 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence cell line Normal3 Fibroblast-like synoviocytes of healthy control subject status: healthy control; cell type: human healthy control synoviocytes cell line controlled vocabulary controlled vocabulary cell line match: cell line

normal_tissue_type healthy donor tissue GSM3685851 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control Normal1 Fibroblast-like synoviocytes of healthy control subject status: healthy control; cell type: human healthy control synoviocytes cell line controlled vocabulary controlled vocabulary normal tissue type match: healthy control

normal_tissue_type healthy donor tissue GSM3685852 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control Normal2 Fibroblast-like synoviocytes of healthy control subject status: healthy control; cell type: human healthy control synoviocytes cell line controlled vocabulary controlled vocabulary normal tissue type match: healthy control

normal_tissue_type healthy donor tissue GSM3685853 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control Normal3 Fibroblast-like synoviocytes of healthy control subject status: healthy control; cell type: human healthy control synoviocytes cell line controlled vocabulary controlled vocabulary normal tissue type match: healthy control

organism Homo sapiens GSE128813 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE128813 dataset_title: The transcriptome analysis of regulatory networks in RA-FLSs organism: Homo sapiens assay_type: microarray processed_data_available: ... keyword match keyword match: homo sapiens

sample_type normal tissue GSM3685851 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control Normal1 Fibroblast-like synoviocytes of healthy control subject status: healthy control; cell type: human healthy control synoviocytes cell line controlled vocabulary controlled vocabulary sample type match: healthy control

sample_type normal tissue GSM3685852 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control Normal2 Fibroblast-like synoviocytes of healthy control subject status: healthy control; cell type: human healthy control synoviocytes cell line controlled vocabulary controlled vocabulary sample type match: healthy control

sample_type normal tissue GSM3685853 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control Normal3 Fibroblast-like synoviocytes of healthy control subject status: healthy control; cell type: human healthy control synoviocytes cell line controlled vocabulary controlled vocabulary sample type match: healthy control

tissue synovium GSE128813 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence synovial dataset_accession: GSE128813 dataset_title: The transcriptome analysis of regulatory networks in RA-FLSs organism: Homo sapiens assay_type: microarray processed_data_available: ... controlled vocabulary controlled vocabulary tissue match: synovial

Sample Group Preview

6 rows shown Show Hide

Study totals: Case 3 | Control 3 | Unassigned 0 | Excluded 0 | Ambiguous 0 6 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Rheumatoid arthritis	Case	GSM3685848	LJR	Fibroblast-like synoviocytes of rheumatoid arthritis Subject status: Rheumatoid arthritis patient; Cell type: Human rheumatoid arthritis synoviocytes cell line	cell line: Standalone model-system marker retained for comparison grouping: cell line.
Rheumatoid arthritis	Case	GSM3685849	RA3	Fibroblast-like synoviocytes of rheumatoid arthritis Subject status: Rheumatoid arthritis patient; Cell type: Human rheumatoid arthritis synoviocytes cell line	cell line: Standalone model-system marker retained for comparison grouping: cell line.
Rheumatoid arthritis	Case	GSM3685850	RA4	Fibroblast-like synoviocytes of rheumatoid arthritis Subject status: Rheumatoid arthritis patient; Cell type: Human rheumatoid arthritis synoviocytes cell line	cell line: Standalone model-system marker retained for comparison grouping: cell line.
Healthy control	Control	GSM3685851	Normal1	Fibroblast-like synoviocytes of healthy control Subject status: Healthy control; Cell type: Human healthy control synoviocytes cell line	cell line: Standalone model-system marker retained for comparison grouping: cell line.
Healthy control	Control	GSM3685852	Normal2	Fibroblast-like synoviocytes of healthy control Subject status: Healthy control; Cell type: Human healthy control synoviocytes cell line	cell line: Standalone model-system marker retained for comparison grouping: cell line.
Healthy control	Control	GSM3685853	Normal3	Fibroblast-like synoviocytes of healthy control Subject status: Healthy control; Cell type: Human healthy control synoviocytes cell line	cell line: Standalone model-system marker retained for comparison grouping: cell line.

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

Related publications

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