Fig. 2.

Volcano plots of the Illumina 27K data showing pairwise comparisons of Turner and Klinefelter samples to male and female samples. The differences in beta values between the respective comparisons is on the X-axis, while the –log10 (p values) is on the Y-axis. Vertical dashed red/green and horizontal blue lines represent the 10 % methylation differences and the 5 % false discovery rates cutoff, respectively. The differentially methylated autosomal CpGs (>10 % differences and FDR <5 %) are represented by red and green filled circles for hypo and hyper methylated loci respectively; their corresponding number is also shown. The verified CpGs by pyrosequencing are represented as blue triangles (1 = cg2487174, 2 = cg16848873, 3 = cg24169822, 4 = cg11418559, 5 = cg20191453, 6 = cg09697795, 7 = cg18059933, 8 = cg26306976, 9 = cg04451770, 10 = cg06812844, 11 = cg04452095; loci labels are as in Fig. 5). Cross-reactive loci, as defined by Chen Y. et al, [54] are labeled with a black “x”. The numbers in each figure correspond to the number of individual CpG sites on autosomes that are hypomethylated (left) and hypermethylated (right); below each number (in parenthesis) is the corresponding number of differentially methylated CpG cites on the X chromosome