Learning Deep Features for DNA Methylation Data Analysis

Many studies demonstrated that the DNA methylation, which occurs in the context of a CpG, has strong correlation with diseases, including cancer. There is a strong interest in analyzing the DNA methylation data to find how to distinguish different subtypes of the tumor. However, the conventional statistical methods are not suitable for analyzing the highly dimensional DNA methylation data with bounded support. In order to explicitly capture the properties of the data, we design a deep neural network, which composes of several stacked binary restricted Boltzmann machines, to learn the low-dimensional deep features of the DNA methylation data. Experimental results show that these features perform best in breast cancer DNA methylation data cluster analysis, compared with some state-of-the-art methods.