Figure 7.

Expression levels are higher for genes in less methylated regions. Each pair of plots shows ratio data for a particular tissue compared with spleen, on two different y-axis scales to help illustrate expression differences. For each tissue comparison, we divided bacterial artificial chromosome (BACs) into three categories of implied relative methylation levels ('High', 'Mid' and 'Low') using median absolute deviation-based thresholds recalculated after averaging ratios across three technical replicates and two donors, if available. Note that low measured array ratios in a BAC-sized genomic region likely reflect more methylation in the test tissue than in spleen, relative to other regions of chromosome 1 with similar GC content, and are therefore labeled as 'High', and vice versa. The boxplots show the distribution of expression ratios reported by Ge et al. [58] for genes whose 5' ends are in BACs of each category. On each plot, the symbol within the bracket represents the P value obtained in a test of the null hypothesis that there is no difference in expression ratios of genes in BACs with 'Low' implied relative methylation levels versus BACs with 'High' relative methylation levels (***, 0 <P < 0.001; **, 0.001 <P < 0.01; *, 0.01 <P < 0.05; ns, P > 0.1, see Methods). The symbol next to the arrow represents the P value obtained in a trend test of whether expression ratios are linearly related to methylation category (coding 'High', 'Mid' and 'Low' categories as -1, 0 and 1, respectively).