Fig. 1

Statistical Methylation Patterns. a Non-Metric multidimensional scaling to identify discriminating cytosine methylation patterns between CP and non-CP cohorts. The first two component axes were plotted to locate the individual subject points in a relative 2D plane. Each point represents the similarity position of a subject based on all potentially informative CpG sites (n = 61,278). CP = orange points; controls = green points. Ellipses represent 90% confidence intervals. The complete segregation of the two cohorts indicates that DNA methylation patterns fundamentally differ between the cohorts. b Comparison of differential methylation load by KEGG functional classification and domain structure. ∆ML (mean difference between CP and control groups) was calculated across the defined length of the gene body structure for six top-level KEGG Pathway Map Classifications: Cellular Processes, Human Diseases, Environmental Information Processing, Genetic Information Processing, Metabolism, and Organismal Systems. Positive ∆ML numbers indicate higher methylation in control subjects and negative numbers indicate higher methylation in CP subjects. Assessing ∆ML score demonstrated a prevalence of altered methylation in 5’ UTR regions for three of the hierarchical KEGG functional categories. Values plotted are means +/− SEM across the number of genes scored in each category