Fig. 3

Clusters of Differential Methylation across four chromosomes. Average methylation percentages are shown at cytosines for patients (blue) and control (pink) samples. The pink and blue lines show the rolling mean methylation score across the fragment length with associated shaded area indicating standard deviation. Larger points indicate sites of differential methylation with a FDR rate corrected Q value < 0.05. Smaller dots sites of differential methylation level of significance > 0.05. Green blocks indicate the detected DMAP fragments with differential methylation. DNase hypersensitivity regions are shown in gray with enhancers shown in red. Regions of enhancer and gene interactions are shown with labels indicating the associated gene. a A 400 bp section of chromosome 17 shows differential methylation overlapping with a DNase hypersensitivity region, an Enhancer (GeneHancer ID: GH17J005769). b A section of chromosome 19 showing the differential methylation falling within DNase hypersensitivity cluster, an enhancer (GeneHancer ID: GH19J005798) and four regulatory interactions. c A section of chromosome 11 showing the closely clustered differential methylation overlapping a DNase hypersensitivity and two regulatory interactions. d 1570 bp section of chromosome 6 showing differential methylation overlapping with DNase hypersensitivity clusters, an enhancer (GeneHancer ID: GH06J000290) and two regulatory interactions. Note in D there is a zoomed view of the chromosome for the individual cytosine cluster (250 bp) and fragment (250 bp) (split by black vertical bar—representing 450 bp)