Fig. 3: Venn diagrams and circular plots illustrating the distinct and overlapping sets of genes associated with differentially methylated sites (DMs) and their chromosome-wise annotation across the genome in four sets of comparisons.
From: Genome-wide methylome-based molecular pathologies associated with depression and suicide
In panel A, the focus is on highlighting the unique genes in proximity to the methylation sites identified when comparing DMs individually obtained from analyses contrasting C vs. MDD+/−S, C vs. MDD−S, C vs. MDD+S, and MDD+S vs. MDD−S. Panel B depicts a Venn diagram showcasing the unique and shared genes in the vicinity of methylation sites resulting from the differential methylation analysis conducted between C vs. MDD+/−S and MDD+S vs. MDD−S. In panels, C–F, Circos plots illustrate the chromosome-wise distribution of the most significant differential methylation site-associated genes following a set of comparisons as mentioned in Fig. 2C–F (C vs. MDD+/−S [C], C vs. MDD−S [D], C vs. MDD+S [E], and MDD−S vs. MDD+S [F]). Like the previous circular plots, each track represents different annotations. The outermost track showcases the genes associated with hyper- and hypomethylated sites. The next concentric track displays hyper-methylated genes in maroon. The second track highlights the p-value distribution (red) for hypermethylated genes. The third track shows the p-value distribution (blue) for hypomethylated genes. The fourth track displays hypomethylated genes in a blue color. The innermost circle represents chromosome number.
