Deep learning for DNase I hypersensitive sites identification

• Main Authors: Chuqiao Lyu, Lei Wang, Juhua Zhang
• Format: Article
• Language: English
• Published: BMC 2018-12-01
• Series: BMC Genomics
• Subjects: DNase I hypersensitive sites; Deep learning; Convolutional neural network
• Online Access: http://link.springer.com/article/10.1186/s12864-018-5283-8

Abstract Background The DNase I hypersensitive sites (DHSs) are associated with the cis-regulatory DNA elements. An efficient method of identifying DHSs can enhance the understanding on the accessibility of chromatin. Despite a multitude of resources available on line including experimental datasets and computational tools, the complex language of DHSs remains incompletely understood. Methods Here, we address this challenge using an approach based on a state-of-the-art machine learning method. We present a novel convolutional neural network (CNN) which combined Inception like networks with a gating mechanism for the response of multiple patterns and longterm association in DNA sequences to predict multi-scale DHSs in Arabidopsis, rice and Homo sapiens. Results Our method obtains 0.961 area under curve (AUC) on Arabidopsis, 0.969 AUC on rice and 0.918 AUC on Homo sapiens. Conclusions Our method provides an efficient and accurate way to identify multi-scale DHSs sequences by deep learning.