Among hypermethylated regions, they included Afap1, Prkce, Atg5, and Tmod1. Among hypomethylated regions, they included Bcas3, Cux1, and Hnrnpu. Consistent with GREAT analysis, Atg5 [39,40] and Cux1 [41,42] interact with the Notch and Hedgehog signaling pathways during normal development and in cancer. The gene discussed is BCAS3; the disease is cancer.