While the majority of the genes did lack differential methylation, we found that certain crucial key regulator genes of cell cycle such as APC, CDKN2A and CDKN2B[28,29,44] are indeed hypermethylated across most tumor types and had an average difference in methylation of at least 20% for three or more cancers (Additional file2: Figure S7). This evidence concerns the gene CDKN2A and cancer.