Fig. 2

Differentially methylated CpG sites in PBMC of SLE patients compared with normal controls by DNA methylation analysis. a Venn diagram showing the number of hypomethylated (left panel) and hypermethylated CpG sites (right panel) in three comparisons, SLE vs. NC, SLE LN⁺ vs. NC, and SLE LN⁻ vs. NC. A total of 1813 hypomethylated CpG sites and 3785 hypermethylated CpG sites are in common in all three comparisons. b The distribution of differentially methylated CpG sites on the genome. The bar charts showed the genomic distribution of hypomethylated (left panel) and hypermethylated (right panel) probes across different genomic regions: TSS1500 and TSS200 (probes located within 1500 and 200 bp from transcription start site, respectively); 5′UTR region; first exon; gene body and 3′UTR region. c Heat maps depicting cluster of the 1065 hypomethylation sites in 333 of 552 upregulated genes, which have one or more hypomethylated CpG sites, and 3024 hypermethylation sites in 487 of 550 downregulated genes, which have one or more hypermethylated sites. NC normal controls, SLE systemic lupus erythematosus, SLE LN ⁺ SLE with lupus nephritis, SLE LN ⁻ SLE without lupus nephritis