Fig. 2.
Global patterns in DNA methylation across visits. a The top principal component (PC1) extracted from the methylome-wide data explained 63.5% of the variance, and the ANOVA plot shows significant differences between the three visits (F2,86 = 5.94, p value = 0.004). b At visit 2, PC1 is correlated with the number of days from surgery to the second visit (r = 0.40, p value = 0.03, n = 31). c The epigenome-wide association plot depicts the location of each CpG (autosomal chromosomes 1 to 22 on the x-axis) and the –log10(p value) for the effect of visit (y-axis). The genome-wide significant threshold was set at p value = 5 × 10-8 (upper red horizontal line); the suggestive threshold was set at p value = 10-5 (lower blue horizontal line). d Distribution of p values for the effect of visit shows a significant deviation from the null hypothesis. e For the CpGs above the suggestive threshold, comparison of mean differences between visit 1 and visit 2 (x-axis), and visit 3 and visit 2 (y-axis) indicates a reversal in methylation patterns from visit 2 to visit 3, with the majority of sites showing lower methylation at visit 2, and then increasing in methylation by visit 3