Identifying DNA Methylation Modules Associated with a Cancer by Probabilistic Evolutionary Learning

DNA methylation leads to inhibition of downstream gene expression. Recently, considerable studies have been made to determine the effects of DNA methylation on complex disease. However, further studies are necessary to find the multiple interactions of many DNA methylation sites and their association with cancer. Here, to assess DNA methylation modules potentially relevant to disease, we use an Estimation of Distribution Algorithm (EDA) to identify high-order interaction of DNA methylated sites (or modules) that are potentially relevant to disease. The method builds a probabilistic dependency model to produce a solution that is a set of discriminative methylation sites. The algorithm is applied to array- and sequencing-based high-throughput DNA methylation profiling datasets. The experimental results show that it is able to identify DNA methylation modules for cancer.