GSE101193

Identify the expression of lncRNAs in peripheral blood mononuclear cells from rheumatoid arthritis

Whole-study status Exploratory only

Dataset can inform exploration but is not strong enough for primary analysis.

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

Comparison type: Tumor vs normal
Contributors: Yuan M, Liu H
Contact name: Min Yuan
Submission date: 2017-07-11
Last update: 2021-07-25
Organization: liaocheng people's hospital
Department: Not available
Public date: 2017-07-12
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: PRJNA393853

Summary

The expression profiles of lncRNAs in peripheral blood mononuclear cells (PBMCs) from rheumatoid arthritis (RA) patients have not been well researched. Therefore, we identified the lncRNA expression profiles in PBMCs from female patients with RA and explored the possible role of the abundantly expressed lncRNAs in RA.

Overall design

3 pairs of samples were mixed with equivalent PBMCs from 27 female RA patients and 27 corresponding healthy controls, which were randomly divided into three groups according to age.

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 Long noncoding RNA profiling revealed differentially expressed lncRNAs associated with disease activity in PBMCs from patients with rheumatoid arthritis. PloS one, 2017 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 ST3GAL3 Promotes the Inflammatory Response of Fibroblast-Like Synoviocytes in Rheumatoid Arthritis by Activating the TLR9/MyD88 Pathway. Mediators of inflammation, 2022 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

Exploratory only Dataset can inform exploration but is not strong enough for primary analysis.

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 biofluid cohort. Derived from current-intent ranking reasons.

Ranking Facts

Supporting evidence

Comparison: Patient biofluid vs healthy control. Specimen: Biofluid. Comparison suitability: 20%.
Interpreted disease metadata: Rheumatoid arthritis.
Processed data is available for downstream review.
External evidence: PubMed links 3 publications; 3 DOIs available: PMID 29140972, PMID 36405992, PMID 36940554.
Publication context: Long noncoding RNA profiling revealed differentially expressed lncRNAs associated with disease activity in PBMCs from patients with rheumatoid arthritis.. PloS one, 2017. PMID 29140972. DOI 10.1371/journal.pone.0186795.
Publication context: ST3GAL3 Promotes the Inflammatory Response of Fibroblast-Like Synoviocytes in Rheumatoid Arthritis by Activating the TLR9/MyD88 Pathway.. Mediators of inflammation, 2022. PMID 36405992. DOI 10.1155/2022/4258742.
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.
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

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

40 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source blood GSM2700240 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: peripheral blood mononuclear cells, rheumatoid arthritis sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2700241 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: peripheral blood mononuclear cells, rheumatoid arthritis sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2700242 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: peripheral blood mononuclear cells, rheumatoid arthritis sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2700243 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: peripheral blood mononuclear cells, healthy control sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2700244 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: peripheral blood mononuclear cells, healthy control sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM2700245 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood source_name: peripheral blood mononuclear cells, healthy control sample-anatomical-source-v1 sample-local anatomical source

assay_type microarray GSE101193 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence microarray dataset_accession: GSE101193 dataset_title: Identify the expression of lncRNAs in peripheral blood mononuclear cells from rheumatoid arthritis organism: Homo sapiens assay_type:... keyword match keyword match: microarray

cell_population peripheral blood mononuclear cells GSM2700240 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood mononuclear cells RA1 peripheral blood mononuclear cells, rheumatoid arthritis disease state: rheumatoid arthritis; cell type: peripheral blood mononuclear cells; gender: female; age: 49y controlled vocabulary controlled vocabulary cell population match: peripheral blood mononuclear cells

cell_population peripheral blood mononuclear cells GSM2700241 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood mononuclear cells RA2 peripheral blood mononuclear cells, rheumatoid arthritis disease state: rheumatoid arthritis; cell type: peripheral blood mononuclear cells; gender: female; age: 49y controlled vocabulary controlled vocabulary cell population match: peripheral blood mononuclear cells

cell_population peripheral blood mononuclear cells GSM2700242 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood mononuclear cells RA3 peripheral blood mononuclear cells, rheumatoid arthritis disease state: rheumatoid arthritis; cell type: peripheral blood mononuclear cells; gender: female; age: 49y controlled vocabulary controlled vocabulary cell population match: peripheral blood mononuclear cells

cell_population peripheral blood mononuclear cells GSM2700243 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood mononuclear cells HC1 peripheral blood mononuclear cells, healthy control disease state: healthy; cell type: peripheral blood mononuclear cells; gender: female; age: 51y controlled vocabulary controlled vocabulary cell population match: peripheral blood mononuclear cells

cell_population peripheral blood mononuclear cells GSM2700244 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood mononuclear cells HC2 peripheral blood mononuclear cells, healthy control disease state: healthy; cell type: peripheral blood mononuclear cells; gender: female; age: 51y controlled vocabulary controlled vocabulary cell population match: peripheral blood mononuclear cells

cell_population peripheral blood mononuclear cells GSM2700245 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood mononuclear cells HC3 peripheral blood mononuclear cells, healthy control disease state: healthy; cell type: peripheral blood mononuclear cells; gender: female; age: 51y controlled vocabulary controlled vocabulary cell population match: peripheral blood mononuclear cells

control_type healthy control GSM2700243 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control HC1 peripheral blood mononuclear cells, healthy control disease state: healthy; cell type: peripheral blood mononuclear cells; gender: female; age: 51y controlled vocabulary controlled vocabulary control type match: healthy control

control_type healthy control GSM2700244 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control HC2 peripheral blood mononuclear cells, healthy control disease state: healthy; cell type: peripheral blood mononuclear cells; gender: female; age: 51y controlled vocabulary controlled vocabulary control type match: healthy control

control_type healthy control GSM2700245 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control HC3 peripheral blood mononuclear cells, healthy control disease state: healthy; cell type: peripheral blood mononuclear cells; gender: female; age: 51y controlled vocabulary controlled vocabulary control type match: healthy control

disease rheumatoid arthritis GSE101193 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis dataset_accession: GSE101193 dataset_title: Identify the expression of lncRNAs in peripheral blood mononuclear cells from rheumatoid arthritis organism: Homo sapiens assay_type:... controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM2700240 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis RA1 peripheral blood mononuclear cells, rheumatoid arthritis disease state: rheumatoid arthritis; cell type: peripheral blood mononuclear cells; gender: female; age: 49y controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM2700241 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis RA2 peripheral blood mononuclear cells, rheumatoid arthritis disease state: rheumatoid arthritis; cell type: peripheral blood mononuclear cells; gender: female; age: 49y controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM2700242 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis RA3 peripheral blood mononuclear cells, rheumatoid arthritis disease state: rheumatoid arthritis; cell type: peripheral blood mononuclear cells; gender: female; age: 49y controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

normal_tissue_type healthy donor tissue GSM2700243 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control HC1 peripheral blood mononuclear cells, healthy control disease state: healthy; cell type: peripheral blood mononuclear cells; gender: female; age: 51y controlled vocabulary controlled vocabulary normal tissue type match: healthy control

normal_tissue_type healthy donor tissue GSM2700244 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control HC2 peripheral blood mononuclear cells, healthy control disease state: healthy; cell type: peripheral blood mononuclear cells; gender: female; age: 51y controlled vocabulary controlled vocabulary normal tissue type match: healthy control

normal_tissue_type healthy donor tissue GSM2700245 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control HC3 peripheral blood mononuclear cells, healthy control disease state: healthy; cell type: peripheral blood mononuclear cells; gender: female; age: 51y controlled vocabulary controlled vocabulary normal tissue type match: healthy control

organism Homo sapiens GSE101193 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE101193 dataset_title: Identify the expression of lncRNAs in peripheral blood mononuclear cells from rheumatoid arthritis organism: Homo sapiens assay_type:... keyword match keyword match: homo sapiens

sample_type normal tissue GSM2700243 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control HC1 peripheral blood mononuclear cells, healthy control disease state: healthy; cell type: peripheral blood mononuclear cells; gender: female; age: 51y controlled vocabulary controlled vocabulary sample type match: healthy control

sample_type normal tissue GSM2700244 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control HC2 peripheral blood mononuclear cells, healthy control disease state: healthy; cell type: peripheral blood mononuclear cells; gender: female; age: 51y controlled vocabulary controlled vocabulary sample type match: healthy control

sample_type normal tissue GSM2700245 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence healthy control HC3 peripheral blood mononuclear cells, healthy control disease state: healthy; cell type: peripheral blood mononuclear cells; gender: female; age: 51y controlled vocabulary controlled vocabulary sample type match: healthy control

specimen_material PBMC preparation GSM2700240 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood mononuclear cells RA1 peripheral blood mononuclear cells, rheumatoid arthritis disease state: rheumatoid arthritis; cell type: peripheral blood mononuclear cells; gender: female; age: 49y controlled vocabulary controlled vocabulary specimen material match: peripheral blood mononuclear cells

specimen_material PBMC preparation GSM2700241 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood mononuclear cells RA2 peripheral blood mononuclear cells, rheumatoid arthritis disease state: rheumatoid arthritis; cell type: peripheral blood mononuclear cells; gender: female; age: 49y controlled vocabulary controlled vocabulary specimen material match: peripheral blood mononuclear cells

specimen_material PBMC preparation GSM2700242 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood mononuclear cells RA3 peripheral blood mononuclear cells, rheumatoid arthritis disease state: rheumatoid arthritis; cell type: peripheral blood mononuclear cells; gender: female; age: 49y controlled vocabulary controlled vocabulary specimen material match: peripheral blood mononuclear cells

specimen_material PBMC preparation GSM2700243 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood mononuclear cells HC1 peripheral blood mononuclear cells, healthy control disease state: healthy; cell type: peripheral blood mononuclear cells; gender: female; age: 51y controlled vocabulary controlled vocabulary specimen material match: peripheral blood mononuclear cells

specimen_material PBMC preparation GSM2700244 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood mononuclear cells HC2 peripheral blood mononuclear cells, healthy control disease state: healthy; cell type: peripheral blood mononuclear cells; gender: female; age: 51y controlled vocabulary controlled vocabulary specimen material match: peripheral blood mononuclear cells

specimen_material PBMC preparation GSM2700245 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence peripheral blood mononuclear cells HC3 peripheral blood mononuclear cells, healthy control disease state: healthy; cell type: peripheral blood mononuclear cells; gender: female; age: 51y controlled vocabulary controlled vocabulary specimen material match: peripheral blood mononuclear cells

tissue blood GSE101193 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood dataset_accession: GSE101193 dataset_title: Identify the expression of lncRNAs in peripheral blood mononuclear cells from rheumatoid arthritis organism: Homo sapiens assay_type:... controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2700240 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood RA1 peripheral blood mononuclear cells, rheumatoid arthritis disease state: rheumatoid arthritis; cell type: peripheral blood mononuclear cells; gender: female; age: 49y controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2700241 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood RA2 peripheral blood mononuclear cells, rheumatoid arthritis disease state: rheumatoid arthritis; cell type: peripheral blood mononuclear cells; gender: female; age: 49y controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2700242 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood RA3 peripheral blood mononuclear cells, rheumatoid arthritis disease state: rheumatoid arthritis; cell type: peripheral blood mononuclear cells; gender: female; age: 49y controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2700243 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood HC1 peripheral blood mononuclear cells, healthy control disease state: healthy; cell type: peripheral blood mononuclear cells; gender: female; age: 51y controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2700244 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood HC2 peripheral blood mononuclear cells, healthy control disease state: healthy; cell type: peripheral blood mononuclear cells; gender: female; age: 51y controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM2700245 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood HC3 peripheral blood mononuclear cells, healthy control disease state: healthy; cell type: peripheral blood mononuclear cells; gender: female; age: 51y controlled vocabulary controlled vocabulary tissue match: blood

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	GSM2700240	RA1	Peripheral blood mononuclear cells, rheumatoid arthritis Disease state: Rheumatoid arthritis; Cell type: Peripheral blood mononuclear cells; Gender: Female; Age: 49y	Case marker detected.
Rheumatoid arthritis	Case	GSM2700241	RA2	Peripheral blood mononuclear cells, rheumatoid arthritis Disease state: Rheumatoid arthritis; Cell type: Peripheral blood mononuclear cells; Gender: Female; Age: 49y	Case marker detected.
Rheumatoid arthritis	Case	GSM2700242	RA3	Peripheral blood mononuclear cells, rheumatoid arthritis Disease state: Rheumatoid arthritis; Cell type: Peripheral blood mononuclear cells; Gender: Female; Age: 49y	Case marker detected.
Healthy control	Control	GSM2700243	HC1	Peripheral blood mononuclear cells, healthy control Disease state: Healthy; Cell type: Peripheral blood mononuclear cells; Gender: Female; Age: 51y	Sample-local control marker detected.
Healthy control	Control	GSM2700244	HC2	Peripheral blood mononuclear cells, healthy control Disease state: Healthy; Cell type: Peripheral blood mononuclear cells; Gender: Female; Age: 51y	Sample-local control marker detected.
Healthy control	Control	GSM2700245	HC3	Peripheral blood mononuclear cells, healthy control Disease state: Healthy; Cell type: Peripheral blood mononuclear cells; Gender: Female; Age: 51y	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