Figure 2

DNAm comparison between sexes on chrX in urothelial bladder cancer (BLCA) samples from TCGA.

(A) DNA methylation status for positions (i.e. probes from the Illumina 450 k array) near TSSs in both sexes from BLCA samples, where the β values (Y-axis) range from 0 (unmethylated) to 1 (fully methylated). The three TSSs are most proximal to the following genes (from top to bottom): XIST, an escapee (ZFX) and a subject gene (HMGB3). Each square represents a sample for the BLCA dataset. Red or blue color represents a female or male sample, respectively. Each violin plot in gray lines shows the distribution of beta values for each sex at each probe. Plots (B,C) show MA plots for chrX probes and autosomal probes on chr7 between sexes, respectively. Each dot represents a probe from the array. M (difference) on y-axis is the logged differential methylation value between sexes, and A (magnitude) on x-axis is the logged average methylation value (as indicated in Methods). The fitted robust regression line is represented in gray, with the corresponding function and correlation reported. Green and red colors in plot (B) represent probes nearest to escapees and subject genes previously reported in Cotton et al. 2015. Gold and gray colors represent probes nearest to XIST and genes not in either three categories. (D) Violin plots showing the distributions of DNA methylation similarity scores between sexes for probes within 50 bps of escTSSs and non-differentially transcribed (nonDT) TSSs on chrX. The similarity score of DNA methylation on y-axis is the residual of M as a function of A on chrX. Only TSSs with at least one probe within 50 bps were plotted, and for those TSSs within 50 bps of multiple probes, the average similarity scores of probes were obtained. The p-value from the Wilcoxon test is reported above the violin plots.