Identification of the differential DNA methylation markers among cancers

DNA methylation plays important roles in the development of cancers. Previous studies have identified the differentially methylated sites (DMSs) between cancer and normal control. However, the methylation variations across multiple cancers have not been revealed. In this study, we identified DMSs among six human cancers (C-DMSs) and DMSs among five normal control tissues (T-DMSs). It is revealed that C-DMSs are highly overlapped with T-DMSs. By excluding the T-DMRs from C-DMRs, 4159 bona fide C-DMSs were selected as methylation variations across multiple cancers. Further analysis confirmed the roles of bona fide C-DMSs in regulation of cancer-related gene expression difference. Moreover, the genes related with these bona fide C-DMSs showed enrichment in the biological processes such as cell membrane components, cell adhesion, cell migration, immune response and cell proliferation, and also the pathways in cancer and bladder cancer. And twenty-eight genes are targeted by hsa-miR-323 which participates in tumorigenesis. In the end, we identified potential cancer-related genes by extracting protein interaction sub-network. This study provides a new framework for mining the potential cancer-specific methylation markers and oncogenes.