Fig. 2

Comparisons of bumphunter and SOMNiBUS results. A Rankings by significance for SOMNiBUS and bumphunter are shown for 127 CpG regions on chromosome X containing at least one overlapping CpG. The size of a point represents the number of overlapping CpG sites. B Average rank score curve of overlapping DMGs on any chromosome identified by both methods. The horizontal axis is the minimum p-value for regions assigned to each of 1183 genes with p < 0.05 by SOMNiBUS. For the 69 genes that were also identified by bumphunter, the vertical axis shows the cumulative average ranks of the bumphunter p-values among their 340 DMGs. When a gene does not match, there is no point shown. The highest average rank was achieved when adding SMAD3, which is colored in red. C Estimated SSc disease effect on CpG methylation (on the logit scale) for the overlapping DMRs identified by both methods at SMAD3. Points (left y-axis) indicate the estimated smoothed coefficient at each individual CpG with intersected positions in red. Pointwise confidence intervals are shown in light gray. Structural gene annotations (right y-axis) are shown in shaded boxes: green (promoters and first exons; both of which are linked to transcriptional silencing), and yellow (1–5 kb upstream of promoters). The width of bumphunter’s DMR is displayed with a red horizontal line, with the average methylation difference in that region indicated just above the line