Figure 5. Significant promoter DNA-methylation differences between sexes within and across breeds.

Heat map columns represent individual tiling arrays, while rows represent significantly differentially methylated (DM) probes adjusted for false discovery rate. Heat maps are organized using hierarchical cluster analysis (average linkage) identifying two major clades both within and across breeds (represented by brackets). A) Probes DM within Red Junglefowl (RJF pools). B) Probes DM within White Leghorn (WL pools). C) Venn-diagram showing how many of the DM probes within breeds that are present across, in both, breeds. D) Probes DM across breeds. Lower case letters next to heat map rows indicate that multiple probes are significantly DM in the same promoter; the same letter indicates the same promoter. Note that “d” and “a” represent probes in the promoters of ZFR and the novel gene in MHM respectively. Each tiling array was hybridized with a pool of six birds.