Supplementary Figure 10: Parent-of-origin methylation and paternal overexpression.

Genes with consistent overexpression from the paternal allele are closer to CpG islands that are preferentially methylated on the maternal allele. To create this plot, CpG islands were first divided into three categories on the basis of data from Xie et al. (Cell 148, 816–831, 2012): those preferentially methylated on the paternal allele (red) or maternal allele (blue) or with no preference (black). The y axis indicates the log of the ratio between two distances: (1) the distance between the TSS of consistently paternally expressed genes and the nearest CpG island and (2) the same measure for inconsistently expressed genes. The distribution of this ratio is plotted for all three categories of CpG islands. The blue line (CpG islands that are preferentially maternally methylated) shows a greater enrichment for negative values (greater area under the curve) than the red line, indicating that genes with consistent paternal expression are generally closer to maternally methylated CpG islands than paternally methylated CpG islands. The sharp downward spikes in each curve are due to the nature of the distance distributions, as many genes have a distance of zero (TSS overlaps a CpG island).