Fig. 4: Single base-scale methylated positions with average and variability.

a Venn diagrams with the number of differentially methylated CpGs (DMCs) and differentially variable CpGs (DVCs). b The distribution of balanced error rates of classification using DMCs or DVCs. Significance levels were estimated from permutation test with 999 Monte Carlo replications. c The largest subnetwork is linked to response to wounding, tissue development, and collagen fibril organization. Yellow areas denote where DMCs or DVCs are concentrated. Colors in large boxes represent gene expression levels in RA relative to OA. Red is upregulated, and green is downregulated. Stacked bar plots represent the number of DMCs or DVCs in certain genes. DMCs are colored red (hypermethylated) and blue (hypomethylated), while DVCs are colored orange (hypervariable) and green (hypovariable). d The second largest subnetwork is related to TGF-β receptor signaling