ArticleJournal of translational medicine2022
Identification of DNA methylation-regulated differentially expressed genes in RA by integrated analysis of DNA methylation and RNA-Seq data.
Article in Journal of translational medicine, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 25 citations in OpenAlex.
- Epigenetic Alterations Beyond CpG Islands in Periodontitis: In Silico Study of DNA Methylation Data.Clinical and experimental dental research · 2026Article
- Article
- Immunological heterogeneity in rheumatoid arthritis: challenges in early-stage stratification, non-response to targeted therapy, and the restoration of immune tolerance.Frontiers in immunology · 2026Review
- Deciphering the interplay between inflammation and dysregulated autophagy in lupus nephritis through network analysis and experimental validation.Frontiers in cell and developmental biology · 2026Article
- A Preclinical State of Graves' Ophthalmopathy Characterized by Hypoxia of T-cells Identified via Multiomics Analysis.The Journal of clinical endocrinology and metabolism · 2025Article
- Analysis of epigenetic biomarkers for diagnosis and assessment of severity in rheumatoid arthritis: a cross-sectional study.Arthritis research & therapy · 2025Article
- Validation of DNA methylation and transcriptional characteristics in CCL5 and CXCL8 genes in autoimmune thyroiditis with varying iodine levels.Scientific reports · 2025Article
- RGS1 Enhancer RNA Promotes Gene Transcription by Recruiting Transcription Factor FOXJ3 and Facilitates Osteoclastogenesis Through PLC-IP3R-dependent CaInflammation · 2025Article
- DNA methylation, combined with RNA sequencing, provide novel insight into molecular classification of chordomas and their microenvironment.Acta neuropathologica communications · 2023Article
- Promoter Methylation-Regulated Differentially Expressed Genes in Breast Cancer.Breast cancer (Dove Medical Press) · 2023Article
- Genome-wide DNA methylation pattern in whole blood of patients with Hashimoto thyroiditis.Frontiers in endocrinology · 2023Article
Corrections and comments
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Authors and funding
10 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
objectiveTo identify novel DNA methylation-regulated differentially expressed genes (MeDEGs) in RA by integrated analysis of DNA methylation and RNA-Seq data.
methodsThe transcription and DNA methylation profiles of 9 RA and 15 OA synovial tissue were generated by RNA-Seq and Illumina 850K DNA methylation BeadChip. Gene set enrichment analysis (GSEA) and Weighted gene co-expression network analysis (WGCNA) were used to analyze methylation-regulated expressed genes by R software. The differentially expressed genes (DEGs), differentially methylated probes (DMPs), differentially methylated genes (DMGs) were analyzed by DESeq and ChAMP R package. The functional correlation of MeDEGs was analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The protein-protein interaction (PPI) network of MeDEGs was constructed by STRING and Reactome FI Cytoscape Plugin. Correlation analysis between methylation level and mRNA expression was conducted with R software.
resultsA total of 17,736 genes, 25,578 methylated genes and 755,852 methylation probes were detected. A total of 16,421 methylation-regulated expressed genes were obtained. The GSEA showed that these genes are associated with activation of immune response, adaptive immune response, Inflammatory response in C5 (ontology gene sets). For KEGG analysis, these genes are associated with rheumatoid arthritis, NF-kappa B signaling pathway, T cell receptor signaling pathway. The WGCNA showed that the turquoise module exhibited the strongest correlation with RA (R = 0.78, P = 1.27 × 10
conclusionsRGS1 can be used as novel methylated biomarkers for RA.
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