GSE189136

Targeting MyD88 Downregulates Inflammatory Mediators and Pathogenic Processes in PBMC From DMARDs-Naïve Rheumatoid Arthritis Patients

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: bulk RNA-seq
Organism: Homo sapiens
Whole-study samples: 19 samples
Specimen: Biofluid
Reported/interpreted study design: Treatment vs control Design classification does not establish patient pairs.

Comparison type: Tumor vs normal
Contributors: Ramirez-Perez S, Bhattaram P
Contact name: Sergio Ramirez-Perez
Submission date: 2021-11-18
Last update: 2022-01-12
Organization: Emory University
Department: Orthopaedics
Public date: 2021-11-30
Experiment types: Expression profiling by high throughput sequencing
Platforms: GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Series type: Series
SubSeries: Not available
BioProject: PRJNA781616

Summary

Purpose: We analyzed RNA-seq from peripheral blood mononuclear cells (PBMC) in DMARDs-naïve RA patients and healthy subjects. Our goal was to evaluate the transcriptional profiles of ST2825-treated PBMC to identify its therapeutic potential. Methods: We analyzed bulk RNA-seq from peripheral blood mononuclear cells (PBMC) in DMARDs-naïve RA patients after stimulation with LPS and IL-1β, PBMC were treated with the MyD88 chemical inhibitor, ST2825. Collection of RNA was performed after 24 h of treatment and samples were sequenced to determine transcriptional changes and regulated processes in treated PBMC. Results: paired-end reads were mapped to the hg19 human genome assembly. RNA levels were normalized using DESeq. We identified 796 differentially expressed (DE) genes by 2-fold change (p<0.05) between RA patients and healthy subjects. Our analysis revealed 631 DE genes between DMARDs-naïve RA patients before and after ST2825 treatment. We identified 471 DE genes between LPS-stimulated RA PBMC and LPS-stimulated RA PBMC treated with ST2825. Conclusion: Our study provides comprehensive evidence supporting the potential application of the MyD88 inhibitor, ST2825, as a modulator of gene expression signtaures involved in pathogenic processes in PBMC from DMARDs-naïve RA patients. Our indepth analysis of RNA-seq data will serve as a valuable resource containing the inflammatory gene expression signatures by MyD88.

Overall design

Identification of the potential effect of ST2825 as an inhibitor of MyD88-dependent gene expression signatures to modulate inflammatory processes in RA patients.

Source Evidence

4 sources

Source	Contribution	Status
GEO	Original dataset metadata, sample metadata, source links, and GEO data availability flags. Sample records 19 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 Targeting MyD88 Downregulates Inflammatory Mediators and Pathogenic Processes in PBMC From DMARDs-Naïve Rheumatoid Arthritis Patients. Frontiers in pharmacology, 2021 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: Treatment status metadata normalized where treatment is part of the comparison. 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

100% 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

10/10 pts

No dataset warnings are present.

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

Standard analyst review

Proceed only after the analyst confirms grouping, exclusions, and source files.

By Siftome standards, no expert review was triggered.

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

Disease context Rheumatoid arthritis Disease context came from Normalization rules.
Likely case group Treated 15 samples
Likely control group Untreated 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: Treatment vs control. Specimen: Biofluid. Comparison suitability: 0%.
Prioritized assay: bulk RNA-seq is the active assay expectation.
Interpreted disease metadata: Rheumatoid arthritis.
Processed data is available for downstream review.
External evidence: PubMed links 1 publication; 1 DOI available: PMID 35002734.
Publication context: Targeting MyD88 Downregulates Inflammatory Mediators and Pathogenic Processes in PBMC From DMARDs-Naïve Rheumatoid Arthritis Patients.. Frontiers in pharmacology, 2021. PMID 35002734. DOI 10.3389/fphar.2021.800220.

Cautions

Downgraded for tissue search because it is a biofluid cohort.
Downgraded for tissue search because it is a treatment/control experiment.
Treatment/control experiment downgraded because this ranking targets tumor-vs-normal tissue comparisons.
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.
Comparison suitability score is below the Phase 1 recommended threshold.

Dataset Warnings

No dataset warnings

Normalized Fields

101 fields

Field Value Source Derived by Confidence Evidence Reason

anatomical_source blood GSM5694892 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5694893 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5694894 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5694895 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5694896 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5694897 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5694898 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5694899 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5694900 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5694901 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5694902 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5694903 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5694904 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5694905 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5694906 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5694907 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5694908 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5694909 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

anatomical_source blood GSM5694910 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence pbmc tissue: PBMC sample-anatomical-source-v1 sample-local anatomical source

assay_type bulk RNA-seq GSE189136 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence bulk rna-seq dataset_accession: GSE189136 dataset_title: Targeting MyD88 Downregulates Inflammatory Mediators and Pathogenic Processes in PBMC From DMARDs-Naïve Rheumatoid Arthritis Patients... keyword match keyword match: bulk rna-seq

cell_population peripheral blood mononuclear cells GSM5694892 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_CS1_UTx PBMC tissue: PBMC; treatment: Untreated; diagnosis: Healthy controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM5694893 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_CS4_UTx PBMC tissue: PBMC; treatment: Untreated; diagnosis: Healthy controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM5694894 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA3_UTx PBMC tissue: PBMC; treatment: Untreated; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM5694895 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA4_UTx PBMC tissue: PBMC; treatment: Untreated; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM5694896 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA2_LPS PBMC tissue: PBMC; treatment: LPS; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM5694897 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA3_LPS PBMC tissue: PBMC; treatment: LPS; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM5694898 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA4_LPS PBMC tissue: PBMC; treatment: LPS; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM5694899 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA2_IL-1B PBMC tissue: PBMC; treatment: IL-1[beta]; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM5694900 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA3_IL-1B PBMC tissue: PBMC; treatment: IL-1[beta]; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM5694901 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA4_IL-1B PBMC tissue: PBMC; treatment: IL-1[beta]; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM5694902 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA2_ST2825 PBMC tissue: PBMC; treatment: ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM5694903 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA3_ST2825 PBMC tissue: PBMC; treatment: ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM5694904 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA4_ST2825 PBMC tissue: PBMC; treatment: ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM5694905 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA2_LPS_ST2825 PBMC tissue: PBMC; treatment: LPS + ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM5694906 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA3_LPS_ST2825 PBMC tissue: PBMC; treatment: LPS + ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM5694907 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA4_LPS_ST2825 PBMC tissue: PBMC; treatment: LPS + ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM5694908 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA2_IL-1B_ST2825 PBMC tissue: PBMC; treatment: IL-1[beta] + ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM5694909 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA3_IL-1B_ST2825 PBMC tissue: PBMC; treatment: IL-1[beta] + ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary cell population match: pbmc

cell_population peripheral blood mononuclear cells GSM5694910 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA4_IL-1B_ST2825 PBMC tissue: PBMC; treatment: IL-1[beta] + ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary cell population match: pbmc

disease rheumatoid arthritis GSE189136 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis dataset_accession: GSE189136 dataset_title: Targeting MyD88 Downregulates Inflammatory Mediators and Pathogenic Processes in PBMC From DMARDs-Naïve Rheumatoid Arthritis Patients... controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM5694894 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis PBMC_RA3_UTx PBMC tissue: PBMC; treatment: Untreated; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM5694895 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis PBMC_RA4_UTx PBMC tissue: PBMC; treatment: Untreated; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM5694896 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis PBMC_RA2_LPS PBMC tissue: PBMC; treatment: LPS; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM5694897 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis PBMC_RA3_LPS PBMC tissue: PBMC; treatment: LPS; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM5694898 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis PBMC_RA4_LPS PBMC tissue: PBMC; treatment: LPS; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM5694899 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis PBMC_RA2_IL-1B PBMC tissue: PBMC; treatment: IL-1[beta]; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM5694900 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis PBMC_RA3_IL-1B PBMC tissue: PBMC; treatment: IL-1[beta]; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM5694901 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis PBMC_RA4_IL-1B PBMC tissue: PBMC; treatment: IL-1[beta]; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM5694902 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis PBMC_RA2_ST2825 PBMC tissue: PBMC; treatment: ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM5694903 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis PBMC_RA3_ST2825 PBMC tissue: PBMC; treatment: ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM5694904 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis PBMC_RA4_ST2825 PBMC tissue: PBMC; treatment: ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM5694905 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis PBMC_RA2_LPS_ST2825 PBMC tissue: PBMC; treatment: LPS + ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM5694906 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis PBMC_RA3_LPS_ST2825 PBMC tissue: PBMC; treatment: LPS + ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM5694907 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis PBMC_RA4_LPS_ST2825 PBMC tissue: PBMC; treatment: LPS + ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM5694908 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis PBMC_RA2_IL-1B_ST2825 PBMC tissue: PBMC; treatment: IL-1[beta] + ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM5694909 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis PBMC_RA3_IL-1B_ST2825 PBMC tissue: PBMC; treatment: IL-1[beta] + ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

disease rheumatoid arthritis GSM5694910 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence rheumatoid arthritis PBMC_RA4_IL-1B_ST2825 PBMC tissue: PBMC; treatment: IL-1[beta] + ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary disease match: rheumatoid arthritis

organism Homo sapiens GSE189136 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence homo sapiens dataset_accession: GSE189136 dataset_title: Targeting MyD88 Downregulates Inflammatory Mediators and Pathogenic Processes in PBMC From DMARDs-Naïve Rheumatoid Arthritis Patients... keyword match keyword match: homo sapiens

specimen_material PBMC preparation GSM5694892 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_CS1_UTx PBMC tissue: PBMC; treatment: Untreated; diagnosis: Healthy controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM5694893 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_CS4_UTx PBMC tissue: PBMC; treatment: Untreated; diagnosis: Healthy controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM5694894 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA3_UTx PBMC tissue: PBMC; treatment: Untreated; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM5694895 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA4_UTx PBMC tissue: PBMC; treatment: Untreated; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM5694896 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA2_LPS PBMC tissue: PBMC; treatment: LPS; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM5694897 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA3_LPS PBMC tissue: PBMC; treatment: LPS; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM5694898 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA4_LPS PBMC tissue: PBMC; treatment: LPS; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM5694899 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA2_IL-1B PBMC tissue: PBMC; treatment: IL-1[beta]; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM5694900 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA3_IL-1B PBMC tissue: PBMC; treatment: IL-1[beta]; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM5694901 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA4_IL-1B PBMC tissue: PBMC; treatment: IL-1[beta]; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM5694902 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA2_ST2825 PBMC tissue: PBMC; treatment: ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM5694903 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA3_ST2825 PBMC tissue: PBMC; treatment: ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM5694904 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA4_ST2825 PBMC tissue: PBMC; treatment: ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM5694905 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA2_LPS_ST2825 PBMC tissue: PBMC; treatment: LPS + ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM5694906 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA3_LPS_ST2825 PBMC tissue: PBMC; treatment: LPS + ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM5694907 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA4_LPS_ST2825 PBMC tissue: PBMC; treatment: LPS + ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM5694908 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA2_IL-1B_ST2825 PBMC tissue: PBMC; treatment: IL-1[beta] + ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM5694909 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA3_IL-1B_ST2825 PBMC tissue: PBMC; treatment: IL-1[beta] + ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary specimen material match: pbmc

specimen_material PBMC preparation GSM5694910 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA4_IL-1B_ST2825 PBMC tissue: PBMC; treatment: IL-1[beta] + ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary specimen material match: pbmc

tissue blood GSE189136 Runtime Siftome inference UNRESOLVED / UNREVIEWED low confidence blood dataset_accession: GSE189136 dataset_title: Targeting MyD88 Downregulates Inflammatory Mediators and Pathogenic Processes in PBMC From DMARDs-Naïve Rheumatoid Arthritis Patients... controlled vocabulary controlled vocabulary tissue match: blood

tissue blood GSM5694892 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_CS1_UTx PBMC tissue: PBMC; treatment: Untreated; diagnosis: Healthy controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM5694893 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_CS4_UTx PBMC tissue: PBMC; treatment: Untreated; diagnosis: Healthy controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM5694894 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA3_UTx PBMC tissue: PBMC; treatment: Untreated; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM5694895 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA4_UTx PBMC tissue: PBMC; treatment: Untreated; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM5694896 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA2_LPS PBMC tissue: PBMC; treatment: LPS; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM5694897 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA3_LPS PBMC tissue: PBMC; treatment: LPS; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM5694898 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA4_LPS PBMC tissue: PBMC; treatment: LPS; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM5694899 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA2_IL-1B PBMC tissue: PBMC; treatment: IL-1[beta]; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM5694900 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA3_IL-1B PBMC tissue: PBMC; treatment: IL-1[beta]; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM5694901 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA4_IL-1B PBMC tissue: PBMC; treatment: IL-1[beta]; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM5694902 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA2_ST2825 PBMC tissue: PBMC; treatment: ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM5694903 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA3_ST2825 PBMC tissue: PBMC; treatment: ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM5694904 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA4_ST2825 PBMC tissue: PBMC; treatment: ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM5694905 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA2_LPS_ST2825 PBMC tissue: PBMC; treatment: LPS + ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM5694906 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA3_LPS_ST2825 PBMC tissue: PBMC; treatment: LPS + ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM5694907 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA4_LPS_ST2825 PBMC tissue: PBMC; treatment: LPS + ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM5694908 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA2_IL-1B_ST2825 PBMC tissue: PBMC; treatment: IL-1[beta] + ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM5694909 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA3_IL-1B_ST2825 PBMC tissue: PBMC; treatment: IL-1[beta] + ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary tissue match: pbmc

tissue blood GSM5694910 Runtime Siftome inference UNRESOLVED / UNREVIEWED medium confidence pbmc PBMC_RA4_IL-1B_ST2825 PBMC tissue: PBMC; treatment: IL-1[beta] + ST2825; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary tissue match: pbmc

treatment_status untreated GSM5694892 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence untreated PBMC_CS1_UTx PBMC tissue: PBMC; treatment: Untreated; diagnosis: Healthy controlled vocabulary controlled vocabulary treatment status match: untreated

treatment_status untreated GSM5694893 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence untreated PBMC_CS4_UTx PBMC tissue: PBMC; treatment: Untreated; diagnosis: Healthy controlled vocabulary controlled vocabulary treatment status match: untreated

treatment_status untreated GSM5694894 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence untreated PBMC_RA3_UTx PBMC tissue: PBMC; treatment: Untreated; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary treatment status match: untreated

treatment_status untreated GSM5694895 Runtime Siftome inference UNRESOLVED / UNREVIEWED high confidence untreated PBMC_RA4_UTx PBMC tissue: PBMC; treatment: Untreated; diagnosis: Rheumatoid arthritis controlled vocabulary controlled vocabulary treatment status match: untreated

Sample Group Preview

19 rows shown Show Hide

Study totals: Case 15 | Control 4 | Unassigned 0 | Excluded 0 | Ambiguous 0 19 rows shown

Group	Role	Accession	Title	Source / characteristics	Reason
Treated	Case	GSM5694896	PBMC_RA2_LPS	PBMC Tissue: PBMC; Treatment: LPS; Diagnosis: Rheumatoid arthritis	Treatment case marker detected.
Treated	Case	GSM5694897	PBMC_RA3_LPS	PBMC Tissue: PBMC; Treatment: LPS; Diagnosis: Rheumatoid arthritis	Treatment case marker detected.
Treated	Case	GSM5694898	PBMC_RA4_LPS	PBMC Tissue: PBMC; Treatment: LPS; Diagnosis: Rheumatoid arthritis	Treatment case marker detected.
Treated	Case	GSM5694899	PBMC_RA2_IL-1B	PBMC Tissue: PBMC; Treatment: IL-1[beta]; Diagnosis: Rheumatoid arthritis	Explicit characteristic comparison arm detected.
Treated	Case	GSM5694900	PBMC_RA3_IL-1B	PBMC Tissue: PBMC; Treatment: IL-1[beta]; Diagnosis: Rheumatoid arthritis	Explicit characteristic comparison arm detected.
Treated	Case	GSM5694901	PBMC_RA4_IL-1B	PBMC Tissue: PBMC; Treatment: IL-1[beta]; Diagnosis: Rheumatoid arthritis	Explicit characteristic comparison arm detected.
ST2825-treated	Case	GSM5694902	PBMC_RA2_ST2825	PBMC Tissue: PBMC; Treatment: ST2825; Diagnosis: Rheumatoid arthritis	Treatment code resolved from the GEO Series design and sample label.
ST2825-treated	Case	GSM5694903	PBMC_RA3_ST2825	PBMC Tissue: PBMC; Treatment: ST2825; Diagnosis: Rheumatoid arthritis	Treatment code resolved from the GEO Series design and sample label.
ST2825-treated	Case	GSM5694904	PBMC_RA4_ST2825	PBMC Tissue: PBMC; Treatment: ST2825; Diagnosis: Rheumatoid arthritis	Treatment code resolved from the GEO Series design and sample label.
ST2825-treated	Case	GSM5694905	PBMC_RA2_LPS_ST2825	PBMC Tissue: PBMC; Treatment: LPS + ST2825; Diagnosis: Rheumatoid arthritis	Treatment code resolved from the GEO Series design and sample label.
ST2825-treated	Case	GSM5694906	PBMC_RA3_LPS_ST2825	PBMC Tissue: PBMC; Treatment: LPS + ST2825; Diagnosis: Rheumatoid arthritis	Treatment code resolved from the GEO Series design and sample label.
ST2825-treated	Case	GSM5694907	PBMC_RA4_LPS_ST2825	PBMC Tissue: PBMC; Treatment: LPS + ST2825; Diagnosis: Rheumatoid arthritis	Treatment code resolved from the GEO Series design and sample label.
ST2825-treated	Case	GSM5694908	PBMC_RA2_IL-1B_ST2825	PBMC Tissue: PBMC; Treatment: IL-1[beta] + ST2825; Diagnosis: Rheumatoid arthritis	Treatment code resolved from the GEO Series design and sample label.
ST2825-treated	Case	GSM5694909	PBMC_RA3_IL-1B_ST2825	PBMC Tissue: PBMC; Treatment: IL-1[beta] + ST2825; Diagnosis: Rheumatoid arthritis	Treatment code resolved from the GEO Series design and sample label.
ST2825-treated	Case	GSM5694910	PBMC_RA4_IL-1B_ST2825	PBMC Tissue: PBMC; Treatment: IL-1[beta] + ST2825; Diagnosis: Rheumatoid arthritis	Treatment code resolved from the GEO Series design and sample label.
Untreated	Control	GSM5694892	PBMC_CS1_UTx	PBMC Tissue: PBMC; Treatment: Untreated; Diagnosis: Healthy	Treatment control marker detected.
Untreated	Control	GSM5694893	PBMC_CS4_UTx	PBMC Tissue: PBMC; Treatment: Untreated; Diagnosis: Healthy	Treatment control marker detected.
Untreated	Control	GSM5694894	PBMC_RA3_UTx	PBMC Tissue: PBMC; Treatment: Untreated; Diagnosis: Rheumatoid arthritis	Treatment control marker detected.
Untreated	Control	GSM5694895	PBMC_RA4_UTx	PBMC Tissue: PBMC; Treatment: Untreated; Diagnosis: Rheumatoid arthritis	Treatment control marker detected.

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External Validation Finder

Carry Siftome's disease, organism, specimen, assay, data type, and accession into a validation project. Uncertain fields remain Unknown.

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Use as Discovery Cohort