Overall methodology. (A) UNC AgilentG4502A_07_03 gene expressed data was analyzed based on the log2 values to obtain the differentially expressed genes. (B) The methylation data from Illumina HumanMethylation27 were classified for each stage. Significantly DNA methylated genes were identified. (C) Stage-specific interaction networks were constructed and annotated with their DNA methylated genes. The nodes and edges of each network were scored based on the topological and biological features. (D) The epigenetic subnetworks were identified and compared across stages to understand the epigenetics commonality and uniqueness.