GSE189338

Expression profile of circRNA in peripheral blood mononuclear cells of patients with rheumatoid arthritis

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: Biofluid
Reported/interpreted study design: Patient biofluid vs healthy control Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Yang J, Lu H, Yang Y, Kuang D, Liu P
Contact name: Junping Yang
Submission date: 2021-11-22
Last update: 2022-04-19
Organization: Jiangxi Chinese Medical University
Department: Laboratory
Public date: 2021-11-30
Experiment types: Non-coding RNA profiling by array
Platforms: GPL21825 074301 Arraystar Human CircRNA microarray V2
Series type: Series
SubSeries: Not available
BioProject: PRJNA782610

Summary

In order to identify new biomarkers for the diagnosis of rheumatoid arthritis, we used circRNA microarray technology to screen the differential expression of circRNA in peripheral blood mononuclear cells of patients with rheumatoid arthritis. We identified a total of 399 differentially expressed circRNAs in RA patients and healthy controls, of which 149 circRNAs were significantly up-regulated in RA patients and 250 were down-regulated. Among them, hsa_circRNA_101328 may be a potential biomarker for the diagnosis of RA.

Overall design

We performed microarray analysis on the circRNAs expression profiles in PBMCs of 4 RA patients and 4 healthy controls.Real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) was used to verify the differential expression of circRNAs in PBMCs of 20 RA patients,10 systemic lupus erythematosus (SLE) patients and 20 age- and gender-matched 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. 3 linked publications 3 DOIs Primary publication Expression profile of circRNA in peripheral blood mononuclear cells of patients with rheumatoid arthritis. BMC medical genomics, 2022 PubMed DOI Related publications Molecular profiling of rheumatoid Arthritis: Expression dynamics of hsa_circ_0092125 and G6PD in an integrative gene expression study. Biochemistry and biophysics reports, 2025 PubMed DOI Construction and Analysis of ceRNA Regulatory Networks Reveal the Core Genes Associated with Rheumatoid Arthritis. International journal of general medicine, 2026 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

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

Secondary RNA assay context should be analyzed separately from ordinary bulk RNA-seq.

Next Steps

Review blockers and update sample grouping or dataset selection before analysis.

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.

Analysis readiness has blockers that must be resolved 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 Lupus erythematosus, rheumatoid arthritis, systemic lupus erythematosus Disease context came from Normalization rules.
Likely case group Rheumatoid arthritis 4 samples
Likely control group Healthy control 4 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: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 0%.
Interpreted disease metadata: Lupus erythematosus, Rheumatoid arthritis, Systemic lupus erythematosus.
Processed data is available for downstream review.
External evidence: PubMed links 3 publications; 3 DOIs available: PMID 35379246, PMID 40778323, PMID 42246038.
Publication context: Expression profile of circRNA in peripheral blood mononuclear cells of patients with rheumatoid arthritis.. BMC medical genomics, 2022. PMID 35379246. DOI 10.1186/s12920-022-01225-9.
Publication context: Molecular profiling of rheumatoid Arthritis: Expression dynamics of hsa_circ_0092125 and G6PD in an integrative gene expression study.. Biochemistry and biophysics reports, 2025. PMID 40778323. DOI 10.1016/j.bbrep.2025.102180.
Publication context: Construction and Analysis of ceRNA Regulatory Networks Reveal the Core Genes Associated with Rheumatoid Arthritis.. International journal of general medicine, 2026. PMID 42246038. DOI 10.2147/IJGM.S589139.

Cautions

Downgraded for tissue search because it is a biofluid cohort.
Downgraded assay: microarray cohorts are separated from the RNA-seq intent.
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.
Small RNA, miRNA, circRNA, or extracellular-vesicle RNA context downgraded for primary mRNA tissue ranking.
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

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

34 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source blood GSM5699428 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: Peripheral blood mononuclear cell sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5699429 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: Peripheral blood mononuclear cell sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5699430 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: Peripheral blood mononuclear cell sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5699431 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: Peripheral blood mononuclear cell sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5699432 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: Peripheral blood mononuclear cell sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5699433 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: Peripheral blood mononuclear cell sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5699434 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: Peripheral blood mononuclear cell sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5699435 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: Peripheral blood mononuclear cell sample-anatomical-source-v1 sample-local anatomical source

assay_type microarray GSE189338 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence microarray dataset_accession: GSE189338 dataset_title: Expression profile of circRNA in peripheral blood mononuclear cells of patients with rheumatoid arthritis organism: Homo sapiens assa... keyword match keyword match: microarray

cell_population peripheral blood mononuclear cells GSM5699428 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood mononuclear cell ExVivoBlood-rheumatoid arthritis1 Peripheral blood mononuclear cell disease state: rheumatoid arthritis; gender: male controlled vocabulary controlled vocabulary cell population match: peripheral blood mononuclear cell

cell_population peripheral blood mononuclear cells GSM5699429 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood mononuclear cell ExVivoBlood-rheumatoid arthritis2 Peripheral blood mononuclear cell disease state: rheumatoid arthritis; gender: male controlled vocabulary controlled vocabulary cell population match: peripheral blood mononuclear cell

cell_population peripheral blood mononuclear cells GSM5699430 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood mononuclear cell ExVivoBlood-rheumatoid arthritis3 Peripheral blood mononuclear cell disease state: rheumatoid arthritis; gender: female controlled vocabulary controlled vocabulary cell population match: peripheral blood mononuclear cell

cell_population peripheral blood mononuclear cells GSM5699431 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood mononuclear cell ExVivoBlood-rheumatoid arthritis4 Peripheral blood mononuclear cell disease state: rheumatoid arthritis; gender: female controlled vocabulary controlled vocabulary cell population match: peripheral blood mononuclear cell

cell_population peripheral blood mononuclear cells GSM5699432 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood mononuclear cell ExVivoBlood-healthy control1 Peripheral blood mononuclear cell disease state: healthy; gender: male controlled vocabulary controlled vocabulary cell population match: peripheral blood mononuclear cell

cell_population peripheral blood mononuclear cells GSM5699433 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood mononuclear cell ExVivoBlood-healthy control2 Peripheral blood mononuclear cell disease state: healthy; gender: male controlled vocabulary controlled vocabulary cell population match: peripheral blood mononuclear cell

cell_population peripheral blood mononuclear cells GSM5699434 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood mononuclear cell ExVivoBlood-healthy control3 Peripheral blood mononuclear cell disease state: healthy; gender: female controlled vocabulary controlled vocabulary cell population match: peripheral blood mononuclear cell

cell_population peripheral blood mononuclear cells GSM5699435 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood mononuclear cell ExVivoBlood-healthy control4 Peripheral blood mononuclear cell disease state: healthy; gender: female controlled vocabulary controlled vocabulary cell population match: peripheral blood mononuclear cell

disease lupus erythematosus GSE189338 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence lupus erythematosus dataset_accession: GSE189338 dataset_title: Expression profile of circRNA in peripheral blood mononuclear cells of patients with rheumatoid arthritis organism: Homo sapiens assa... controlled vocabulary controlled vocabulary disease match: lupus erythematosus

disease rheumatoid arthritis GSE189338 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis dataset_accession: GSE189338 dataset_title: Expression profile of circRNA in peripheral blood mononuclear cells of patients with rheumatoid arthritis organism: Homo sapiens assa... controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease systemic lupus erythematosus GSE189338 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence systemic lupus erythematosus dataset_accession: GSE189338 dataset_title: Expression profile of circRNA in peripheral blood mononuclear cells of patients with rheumatoid arthritis organism: Homo sapiens assa... controlled vocabulary controlled vocabulary disease match: systemic lupus erythematosus

disease rheumatoid arthritis GSM5699428 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis ExVivoBlood-rheumatoid arthritis1 Peripheral blood mononuclear cell disease state: rheumatoid arthritis; gender: male controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM5699429 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis ExVivoBlood-rheumatoid arthritis2 Peripheral blood mononuclear cell disease state: rheumatoid arthritis; gender: male controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM5699430 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis ExVivoBlood-rheumatoid arthritis3 Peripheral blood mononuclear cell disease state: rheumatoid arthritis; gender: female controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM5699431 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis ExVivoBlood-rheumatoid arthritis4 Peripheral blood mononuclear cell disease state: rheumatoid arthritis; gender: female controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

organism Homo sapiens GSE189338 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE189338 dataset_title: Expression profile of circRNA in peripheral blood mononuclear cells of patients with rheumatoid arthritis organism: Homo sapiens assa... keyword match keyword match: homo sapiens

tissue blood GSE189338 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood dataset_accession: GSE189338 dataset_title: Expression profile of circRNA in peripheral blood mononuclear cells of patients with rheumatoid arthritis organism: Homo sapiens assa... controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM5699428 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood ExVivoBlood-rheumatoid arthritis1 Peripheral blood mononuclear cell disease state: rheumatoid arthritis; gender: male controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM5699429 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood ExVivoBlood-rheumatoid arthritis2 Peripheral blood mononuclear cell disease state: rheumatoid arthritis; gender: male controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM5699430 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood ExVivoBlood-rheumatoid arthritis3 Peripheral blood mononuclear cell disease state: rheumatoid arthritis; gender: female controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM5699431 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood ExVivoBlood-rheumatoid arthritis4 Peripheral blood mononuclear cell disease state: rheumatoid arthritis; gender: female controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM5699432 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood ExVivoBlood-healthy control1 Peripheral blood mononuclear cell disease state: healthy; gender: male controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM5699433 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood ExVivoBlood-healthy control2 Peripheral blood mononuclear cell disease state: healthy; gender: male controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM5699434 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood ExVivoBlood-healthy control3 Peripheral blood mononuclear cell disease state: healthy; gender: female controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM5699435 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood ExVivoBlood-healthy control4 Peripheral blood mononuclear cell disease state: healthy; gender: female controlled vocabulary controlled vocabulary tissue match: blood

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	GSM5699428	ExVivoBlood-rheumatoid arthritis1	Peripheral blood mononuclear cell Disease state: Rheumatoid arthritis; Gender: Male	Case marker detected.
Rheumatoid arthritis	Case	GSM5699429	ExVivoBlood-rheumatoid arthritis2	Peripheral blood mononuclear cell Disease state: Rheumatoid arthritis; Gender: Male	Case marker detected.
Rheumatoid arthritis	Case	GSM5699430	ExVivoBlood-rheumatoid arthritis3	Peripheral blood mononuclear cell Disease state: Rheumatoid arthritis; Gender: Female	Case marker detected.
Rheumatoid arthritis	Case	GSM5699431	ExVivoBlood-rheumatoid arthritis4	Peripheral blood mononuclear cell Disease state: Rheumatoid arthritis; Gender: Female	Case marker detected.
Healthy control	Control	GSM5699432	ExVivoBlood-healthy control1	Peripheral blood mononuclear cell Disease state: Healthy; Gender: Male	Sample-local control marker detected.
Healthy control	Control	GSM5699433	ExVivoBlood-healthy control2	Peripheral blood mononuclear cell Disease state: Healthy; Gender: Male	Sample-local control marker detected.
Healthy control	Control	GSM5699434	ExVivoBlood-healthy control3	Peripheral blood mononuclear cell Disease state: Healthy; Gender: Female	Sample-local control marker detected.
Healthy control	Control	GSM5699435	ExVivoBlood-healthy control4	Peripheral blood mononuclear cell Disease state: Healthy; Gender: Female	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

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