Figure 4
Differential DNA methylation analysis. (A) Volcano plot visualizing DMCs. Percentage of methylation difference is represented on the x-axis, while the − log10(p value) is represented on the y-axis. Hypermethylated CpGs and hypomethylated CpGs are represented in red and blue, respectively. The horizontal dashed line corresponds to − log10(0.05) to represent a threshold for significance. The chart on the bottom demonstrates the numbers of differentially methylated sites in each comparison. (B) Pie charts represent the genomic feature distribution of the DMCs from each comparison. Labels within each section represent the % of DMCs that fall within these features. TTS stands for transcription termination site. (C,D,E,F) The top 10 ranked over-represented KEGG pathways of genes that contain DMCs within their boundary (from 2000 bp upstream of the transcription start site to 1000 bp downstream of the transcription termination site) for the comparisons of “Attacker” vs “Parental” (C), “Attacker” vs “Father” (D), “Parental” vs “Father” (E), and “Father” vs “Mother” (F). In each of the panels, the vertical dashed line represents an FDR cutoff of 0.05, and the color represents the enrichment ratio of the pathways.
