Fig. 4

Subtypes of patients with knee OA showed differences in enhancer methylation related to osteoarthritis phenotypes. a Principal component analysis of patients with knee OA based on the methylation profiles of 8111 DMCs. First, two principal components (PC1 and PC2) were used to show the classification of the knee OA samples. b Volcano plot of the mean methylation differences between two knee groups. Red dots represent the eDMCs identified by t tests. c Two-way hierarchical clustering of methylation in group-specific eDMCs across the knee OA samples. Each row represents a group-specific eDMC, and each column represents a sample. For each sample, the age is represented by a gradual color from green (young) to red (old), the gender is indicated by purple for females and blue for males, and the group was colored by two colors that are the same as those in Figure a. DNA methylation (β value) is represented by a color from dark blue (unmethylated) to dark red (fully methylated). d Human phenotypes (HP) and disease ontologies (DO) enriched by nearby genes of the eDMCs. The length of each bar represents the significance of the phenotype enriched in the eDMCs. The right panel shows the eDMC-gene pair for the eDMCs enriched in osteoarthritis as a human phenotype and disease ontology