GSE134087

Analysis of differential expression profiles of Long noncoding RNA in peripheral blood of patients with active 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

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: 4 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: Li M, Ma K
Contact name: Ming Li
Submission date: 2019-07-10
Last update: 2020-06-10
Organization: Nanjing University of Chinese Medicine
Department: Not available
Public date: 2020-06-10
Experiment types: Expression profiling by array; Non-coding RNA profiling by array
Platforms: GPL16956 Agilent-045997 Arraystar human lncRNA microarray V3 (Probe Name Version)
Series type: Series
SubSeries: Not available
BioProject: PRJNA553755

Summary

we studied the expression profile of lncRNA in peripheral blood of patients with active RA LncRNA and mRNA expression in peripheral blood from two activity RA patients and two healthy donors were analyzed with microarray profiling. peripheral blood of five active RA patients and five healthy control members were collected. Quantitative real-time PCR was further used to screen and verify the expression of lncRNA to verify the expression of the selected lncRNA; perform bioinformatics analysis to study the potential function of the differentially expressed genes, construct a receiver operating characteristic (ROC) curve to evaluate the clinical diagnostic value of the identified lncRNA, and use correlation analysis to explore the relationship between aberrantly expressed lncRNA that may have diagnostic value and clinical indicators.

Overall design

Two RA patients were used as the RA group, and two healthy people were used as the control group, and 6 ml of peripheral blood were collected respectively.,then perform LncRNAs chips by Arraystar Human LncRNAs chip (Arraystar)

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 4 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. 2 linked publications 2 DOIs Primary publication Differential long non-coding RNA expression profiles in the peripheral blood and CD4(+) T cells of patients with active rheumatoid arthritis. Experimental and therapeutic medicine, 2020 PubMed DOI Related publications Identification and preliminary validation of synovial tissue-specific genes and their-mediated biological mechanisms in rheumatoid arthritis. International immunopharmacology, 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

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.

Small cohort warning is present.

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 2 samples
Likely control group Healthy control 2 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: Rheumatoid arthritis.
Processed data is available for downstream review.
External evidence: PubMed links 2 publications; 2 DOIs available: PMID 32509015, PMID 36940554.
Publication context: Differential long non-coding RNA expression profiles in the peripheral blood and CD4(+) T cells of patients with active rheumatoid arthritis.. Experimental and therapeutic medicine, 2020. PMID 32509015. DOI 10.3892/etm.2020.8681.
Publication context: Identification and preliminary validation of synovial tissue-specific genes and their-mediated biological mechanisms in rheumatoid arthritis.. International immunopharmacology, 2023. PMID 36940554. DOI 10.1016/j.intimp.2023.109997.

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.
Overall score capped because comparison suitability is weak for the selected search intent.
Overall score capped because fewer than six samples are too small for top-ranked 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

Dataset has fewer than six samples and should not be treated as a high-confidence cohort without manual review.
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

24 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source blood GSM3936838 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood tissue: whole blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM3936839 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood tissue: whole blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM3936840 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood tissue: whole blood sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM3936841 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood tissue: whole blood sample-anatomical-source-v1 sample-local anatomical source

assay_type microarray GSE134087 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence microarray dataset_accession: GSE134087 dataset_title: Analysis of differential expression profiles of Long noncoding RNA in peripheral blood of patients with active rheumatoid arthritis o... keyword match keyword match: microarray

control_type healthy control GSM3936840 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control peripheral blood_HC_rep1-1 peripheral blood_HC_rep1-1 tissue: whole blood; gender: male; diagnosis: healthy control controlled vocabulary controlled vocabulary control type match: healthy control

control_type healthy control GSM3936841 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control peripheral blood_HC_rep1-2 peripheral blood_HC_rep1-2 tissue: whole blood; gender: female; diagnosis: healthy control controlled vocabulary controlled vocabulary control type match: healthy control

disease rheumatoid arthritis GSE134087 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis dataset_accession: GSE134087 dataset_title: Analysis of differential expression profiles of Long noncoding RNA in peripheral blood of patients with active rheumatoid arthritis o... controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM3936838 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis peripheral blood_RA_rep1-1 peripheral blood_RA_rep1-1 tissue: whole blood; gender: male; diagnosis: rheumatoid arthritis controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM3936839 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis peripheral blood_RA_rep1-2 peripheral blood_RA_rep1-2 tissue: whole blood; gender: female; diagnosis: rheumatoid arthritis controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

normal_tissue_type healthy donor tissue GSM3936840 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control peripheral blood_HC_rep1-1 peripheral blood_HC_rep1-1 tissue: whole blood; gender: male; diagnosis: healthy control controlled vocabulary controlled vocabulary normal tissue type match: healthy control

normal_tissue_type healthy donor tissue GSM3936841 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control peripheral blood_HC_rep1-2 peripheral blood_HC_rep1-2 tissue: whole blood; gender: female; diagnosis: healthy control controlled vocabulary controlled vocabulary normal tissue type match: healthy control

organism Homo sapiens GSE134087 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE134087 dataset_title: Analysis of differential expression profiles of Long noncoding RNA in peripheral blood of patients with active rheumatoid arthritis o... keyword match keyword match: homo sapiens

sample_type normal tissue GSM3936840 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control peripheral blood_HC_rep1-1 peripheral blood_HC_rep1-1 tissue: whole blood; gender: male; diagnosis: healthy control controlled vocabulary controlled vocabulary sample type match: healthy control

sample_type normal tissue GSM3936841 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control peripheral blood_HC_rep1-2 peripheral blood_HC_rep1-2 tissue: whole blood; gender: female; diagnosis: healthy control controlled vocabulary controlled vocabulary sample type match: healthy control

specimen_material whole blood GSM3936838 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood peripheral blood_RA_rep1-1 peripheral blood_RA_rep1-1 tissue: whole blood; gender: male; diagnosis: rheumatoid arthritis controlled vocabulary controlled vocabulary specimen material match: whole blood

specimen_material whole blood GSM3936839 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood peripheral blood_RA_rep1-2 peripheral blood_RA_rep1-2 tissue: whole blood; gender: female; diagnosis: rheumatoid arthritis controlled vocabulary controlled vocabulary specimen material match: whole blood

specimen_material whole blood GSM3936840 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood peripheral blood_HC_rep1-1 peripheral blood_HC_rep1-1 tissue: whole blood; gender: male; diagnosis: healthy control controlled vocabulary controlled vocabulary specimen material match: whole blood

specimen_material whole blood GSM3936841 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence whole blood peripheral blood_HC_rep1-2 peripheral blood_HC_rep1-2 tissue: whole blood; gender: female; diagnosis: healthy control controlled vocabulary controlled vocabulary specimen material match: whole blood

tissue blood GSE134087 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood dataset_accession: GSE134087 dataset_title: Analysis of differential expression profiles of Long noncoding RNA in peripheral blood of patients with active rheumatoid arthritis o... controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM3936838 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood peripheral blood_RA_rep1-1 peripheral blood_RA_rep1-1 tissue: whole blood; gender: male; diagnosis: rheumatoid arthritis controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM3936839 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood peripheral blood_RA_rep1-2 peripheral blood_RA_rep1-2 tissue: whole blood; gender: female; diagnosis: rheumatoid arthritis controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM3936840 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood peripheral blood_HC_rep1-1 peripheral blood_HC_rep1-1 tissue: whole blood; gender: male; diagnosis: healthy control controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM3936841 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood peripheral blood_HC_rep1-2 peripheral blood_HC_rep1-2 tissue: whole blood; gender: female; diagnosis: healthy control controlled vocabulary controlled vocabulary tissue match: blood

Sample Group Preview

4 rows shown Show Hide

Study totals: Case 2 | Control 2 | Unassigned 0 | Excluded 0 | Ambiguous 0 4 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Rheumatoid arthritis	Case	GSM3936838	Peripheral blood_RA_rep1-1	Peripheral blood_RA_rep1-1 Tissue: Whole blood; Gender: Male; Diagnosis: Rheumatoid arthritis	Explicit sample label case marker detected.
Rheumatoid arthritis	Case	GSM3936839	Peripheral blood_RA_rep1-2	Peripheral blood_RA_rep1-2 Tissue: Whole blood; Gender: Female; Diagnosis: Rheumatoid arthritis	Explicit sample label case marker detected.
Healthy control	Control	GSM3936840	Peripheral blood_HC_rep1-1	Peripheral blood_HC_rep1-1 Tissue: Whole blood; Gender: Male; Diagnosis: Healthy control	Sample-local control marker detected.
Healthy control	Control	GSM3936841	Peripheral blood_HC_rep1-2	Peripheral blood_HC_rep1-2 Tissue: Whole blood; Gender: Female; Diagnosis: Healthy 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.

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