While recent integrative analyses of copy-number and gene expression data in breast cancer have revealed a complex molecular landscape with multiple subtypes and many oncogenic/tumour suppressor driver events, much less is known about the role of DNA methylation in shaping breast cancer taxonomy and defining driver events.Here we applied a functional supervised algorithm called FEM, which performs a systems-level integration of DNA methylation and gene expression data, to matched DNA methylation and RNA-Seq breast cancer data from the TCGA project, in order to identify putative epigenetic driver events and to explore the resulting molecular taxonomy.