BiLSTM-5mC: A Bidirectional Long Short-Term Memory-Based Approach for Predicting 5-Methylcytosine Sites in Genome-Wide DNA Promoters

Abstract

An important reason of cancer proliferation is the change in DNA methylation patterns, characterized by the localized hypermethylation of the promoters of tumor-suppressor genes together with an overall decrease in the level of 5-methylcytosine (5mC). Therefore, identifying the 5mC sites in the promoters is a critical step towards further understanding the diverse functions of DNA methylation in genetic diseases such as cancers and aging. However, most wet-lab experimental techniques are often time consuming and laborious for detecting 5mC sites. In this study, we proposed a deep learning-based approach, called BiLSTM-5mC, for accurately identifying 5mC sites in genome-wide DNA promoters. First, we randomly divided the negative samples into 11 subsets of equal size, one of which can form the balance subset by combining with the positive samples in the same amount. Then, two types of feature vectors encoded by the one-hot method, and the nucleotide property and frequency (NPF) methods were fed into a bidirectional long short-term memory (BiLSTM) network and a full connection layer to train the 22 submodels. Finally, the outputs of these models were integrated to predict 5mC sites by using the majority vote strategy. Our experimental results demonstrated that BiLSTM-5mC outperformed existing methods based on the same independent dataset.

Keywords

• 5-methylcytosine sites
• one-hot encoding
• nucleotide property and frequency
• bidirectional long short-term memory
• majority vote