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Among the thousands of gene promoters hyper- or hypomethylated in cancer genomes, only a small portion of them play “driver” roles in tumorigenesis, whereas the others are only “passengers”. Here, we develop an approach to identify driver methylation genes of cancer with integrated promoter methylation and gene expression data generated from paired cancer and normal samples for each of a cohort of breast cancer patients, taking the advantage that data of paired samples could provide the relative gene methylation change information from normal to tumor for each individual patient. We applied this approach to analyze a dataset of breast cancer and discovered some novel cancer driver genes. The identified driver genes with methylation alteration may help us to reveal new molecular targets for potential epigenetic therapy

Identifying Driver Genes of Breast Cancer by Integrated Analysis of Methylation and Expression Data in Paired Disease-Normal Samples of Patients