Jianwei Hong1,2, Ruitian Gao3, Yang Yang1,4. 1. Department of Computer Science and Engineering, Shanghai Jiao Tong University, 800 Dong Chuan Rd., Shanghai 200240, China. 2. School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China. 3. Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, Shanghai 200240, China. 4. Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering, Shanghai, 200240, China.
Abstract
MOTIVATION: Enhancers are important functional elements in genome sequences. The identification of enhancers is a very challenging task due to the great diversity of enhancer sequences and the flexible localization on genomes. Till now, the interactions between enhancers and genes have not been fully understood yet. To speed up the studies of the regulatory roles of enhancers, computational tools for the prediction of enhancers have emerged in recent years. Especially, thanks to the ENCODE project and the advances of high-throughput experimental techniques, a large amount of experimentally verified enhancers have been annotated on the human genome, which allows large-scale predictions of unknown enhancers using data-driven methods. However, except for human and some model organisms, the validated enhancer annotations are scarce for most species, leading to more difficulties in the computational identification of enhancers for their genomes. RESULTS: In this study, we propose a deep learning-based predictor for enhancers, named CrepHAN, which is featured by a hierarchical attention neural network and word embedding-based representations for DNA sequences. We use the experimentally-supported data of the human genome to train the model, and perform experiments on human and other mammals, including mouse, cow, and dog. The experimental results show that CrepHAN has more advantages on cross-species predictions, and outperforms the existing models by a large margin. Especially, for human-mouse cross-predictions, the AUC score of ROC curve is increased by 0.033∼0.145 on the combined tissue dataset and 0.032∼0.109 on tissue-specific datasets. AVAILABILITY: bcmi.sjtu.edu.cn/~yangyang/CrepHAN.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: Enhancers are important functional elements in genome sequences. The identification of enhancers is a very challenging task due to the great diversity of enhancer sequences and the flexible localization on genomes. Till now, the interactions between enhancers and genes have not been fully understood yet. To speed up the studies of the regulatory roles of enhancers, computational tools for the prediction of enhancers have emerged in recent years. Especially, thanks to the ENCODE project and the advances of high-throughput experimental techniques, a large amount of experimentally verified enhancers have been annotated on the human genome, which allows large-scale predictions of unknown enhancers using data-driven methods. However, except for human and some model organisms, the validated enhancer annotations are scarce for most species, leading to more difficulties in the computational identification of enhancers for their genomes. RESULTS: In this study, we propose a deep learning-based predictor for enhancers, named CrepHAN, which is featured by a hierarchical attention neural network and word embedding-based representations for DNA sequences. We use the experimentally-supported data of the human genome to train the model, and perform experiments on human and other mammals, including mouse, cow, and dog. The experimental results show that CrepHAN has more advantages on cross-species predictions, and outperforms the existing models by a large margin. Especially, for human-mouse cross-predictions, the AUC score of ROC curve is increased by 0.033∼0.145 on the combined tissue dataset and 0.032∼0.109 on tissue-specific datasets. AVAILABILITY: bcmi.sjtu.edu.cn/~yangyang/CrepHAN.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.