DMAK: A curated pan-cancer DNA methylation annotation knowledgebase

Pan-cancer analysis can identify cell- and tissue-specific genomic loci and regions with underlying biological functions. Here we present an online curated DNA Methylation Annotation Knowledgebase, DMAK, which includes the pan-cancer analysis results for differentially-methylated loci and regions by the Reduced Representation Bisulfite Sequencing profiling technology. DMAK contains 3 modules of curated information and analysis results on 688,445 CpG sites across 19 cancer and embryonic stem cell lines from ENCODE, and further analysis of survival associations with clinical sources retrieved from TCGA. The knowledgebase covers all identified differentially-methylated CpG sites and regions of interest, further annotated genomic information, together with tumor suppressor genes information and calculated methylation level. DMAK provides meaningful clues for deriving functional association network and related clinical association results based on protein-coding genes, including tumor suppressor genes, identified from differentially methylated regions of interest. Thus DMAK constitutes a comprehensive reference source for the current epigenetic research and clinical study.