Background: DNA methylation plays a crucial role in the occurrence of complex diseases.Genes that interact directly or indirectly may have the same or similar functions in the biological processes in which they are involved and together contribute to the related disease phenotypes.The complicated relations between genes can be clearly represented using network theory.A protein-protein interaction (PPI) network offers a platform from which to systematically identify disease-related genes from the relations between genes with similar functions.Methods: A weighted human PPI network (WHPN) is constructed using DNA methylation correlations based on human protein-protein interactions.A cancer-associated subnetwork (CASN) is obtained from WHPN by selecting genes associated with seed genes which were known to be methylated in the four cancers.Using neighborhood-weighting decision rule, the potential cancer-related genes are prioritized, and than are carried to functional analysis.It provides a comprehensive approach for prioritizing the cancer-related genes with abnormal methylation from genome and epigenome data.Results: WHPN that we built represents the relationships of DNA methylation levels in gene pairs for four cancer types.And we found that CASN had a more densely connected network community than WHPN, indicating that the genes in CASN were much closer to seed genes.We prioritized 154 potential cancer-related genes with aberrant methylation in CASN.A function enrichment analysis for GO and KEGG indicated that the optimized genes were mainly involved in the biological processes of regulating cell apoptosis and programmed cell death.An analysis of expression profiling data revealed that many of the optimized genes were expressed differentially in the four cancers.By examining the PubMed co-citations, we found 43 optimized genes were related with cancers and aberrant methylation, and 10 genes were validated to be methylated aberrantly in cancers.Of 154 optimized genes, 27 were as diagnostic markers and 20 as prognostic markers previously identified in literature for cancers and other complex diseases by searching PubMed manually.We found that 31 of the optimized genes were targeted as drug response markers in DrugBank.Conclusions: Here we have shown that network theory combined with epigenetic characteristics provides a favorable platform from which to identify cancer-related genes.We prioritized 154 potential cancer-related genes with aberrant methylation that might contribute to the further understanding of cancers .