Figure 7

Non-random location of differential methylation. (A) Enrichment ratios (log2 transformed) for differential methylation loci (DML) within the indicated gene and genomic features. The associated p-values for enrichment or depletion indicated above the plot were determined by Fischer’s exact test (hypergeometric distribution). The bar colors map to the total number of DML within the respective regions (scale bar on right axis). (B) Enrichment probabilities (hypergeometric, adjusted for multiple testing using Holm’s method and −log10 transformed) of overlapping 1000 bp windows either side of TSSs. Upper section indicates the TSS (arrow) and the regions used in the calculation. p-values indicate the probability of observing the observed number or larger of DMLs (p < 0.05) within each window given the total number of measurements falling within the windows and the total number of DMLs. (C) Mean differential methylation around TSSs. The mean of absolute DSS test statistics observed around TSSs. Each point indicates the mean value at the specific distance. The red line is a kernel smoothed mean for the points. Colors of points indicates the sampling density (i.e. the number of measurements contributing to each mean value), with values mapping from low to high from blue to purple via cyan, green, yellow and red. (D) Differential methylation around the first exon of the gene ppp2r2ba (protein phosphatase 2, regulatory subunit B, beta a), overlapping an intron of igfbp7 (insulin-like growth factor binding protein 7) gene located on chromosome 14. Each point indicates mean methylation measurement in each of the six samples per group, red and green points indicate DNA methylation for the control and low 1-C samples, respectively. The point size maps to the number of reads used to derive the methylation level estimate. The ppp2r2ba gene is transcribed from right to left in the plot. Lower panel gives an expanded view of the genomic locus containing ppp2r2ba.