CapsEnhancer: An Effective Computational Framework for Identifying Enhancers Based on Chaos Game Representation and Capsule Network

• Published in: Journal of chemical information and modeling 2024-07, Vol.64 (14), p.5725-5736
• Main Authors: Yao, Lantian, Xie, Peilin, Guan, Jiahui, Chung, Chia-Ru, Huang, Yixian, Pang, Yuxuan, Wu, Huacong, Chiang, Ying-Chih, Lee, Tzong-Yi
• Format: Article
• Language: English
• Subjects: Bioinformatics; Biological effects; Computational Biology - methods; Computer vision; Deep Learning; Deoxyribonucleic acid; DNA; Enhancer Elements, Genetic; Gene expression; Gene sequencing; Humans; Nonlinear Dynamics; Representations
• ISSN: 1549-9596; 1549-960X; 1549-960X
• DOI: 10.1021/acs.jcim.4c00546

Enhancers are a class of noncoding DNA, serving as crucial regulatory elements in governing gene expression by binding to transcription factors. The identification of enhancers holds paramount importance in the field of biology. However, traditional experimental methods for enhancer identification demand substantial human and material resources. Consequently, there is a growing interest in employing computational methods for enhancer prediction. In this study, we propose a two-stage framework based on deep learning, termed CapsEnhancer, for the identification of enhancers and their strengths. CapsEnhancer utilizes chaos game representation to encode DNA sequences into unique images and employs a capsule network to extract local and global features from sequence “images”. Experimental results demonstrate that CapsEnhancer achieves state-of-the-art performance in both stages. In the first and second stages, the accuracy surpasses the previous best methods by 8 and 3.5%, reaching accuracies of 94.5 and 95%, respectively. Notably, this study represents the pioneering application of computer vision methods to enhancer identification tasks. Our work not only contributes novel insights to enhancer identification but also provides a fresh perspective for other biological sequence analysis tasks.