论文标题
EPIHC:通过使用混合功能和交流学习来改善增强器促销的交互预测
EPIHC: Improving Enhancer-Promoter Interaction Prediction by using Hybrid features and Communicative learning
论文作者
论文摘要
增强子促进剂相互作用(EPIP)调节细胞中特定基因的表达,而EPIS对于理解基因调节,细胞分化和疾病机制很重要。通过湿实验的EPI识别是昂贵且耗时的,并且需要计算方法。在本文中,我们基于序列衍生的特征和EPI预测的基因组特征提出了一种基于神经网络的方法EPIHC。 EPIHC分别使用卷积神经网络(CNN)从增强子和启动子序列中提取特征,然后设计一个交流学习模块,以捕获增强子和启动子序列之间的交流信息。 EPIHC还考虑了增强子和启动子的基因组特征。最后,EPIHC结合了序列衍生的特征和基因组特征,以预测EPIS。计算实验表明,EPIHC的表现优于基准数据集和染色体分解数据集上现有的最新EPI预测方法,研究表明,交流学习模块可以带来有关CNN忽略的有关EPIS的明确信息。此外,我们考虑了两种在跨细胞线预测中提高EPIHC的性能的策略,实验结果表明,在训练细胞系上构建的EPIHC表现出改善其他细胞系的性能。
Enhancer-promoter interactions (EPIs) regulate the expression of specific genes in cells, and EPIs are important for understanding gene regulation, cell differentiation and disease mechanisms. EPI identification through the wet experiments is costly and time-consuming, and computational methods are in demand. In this paper, we propose a deep neural network-based method EPIHC based on sequence-derived features and genomic features for the EPI prediction. EPIHC extracts features from enhancer and promoter sequences respectively using convolutional neural networks (CNN), and then design a communicative learning module to captures the communicative information between enhancer and promoter sequences. EPIHC also take the genomic features of enhancers and promoters into account. At last, EPIHC combines sequence-derived features and genomic features to predict EPIs. The computational experiments show that EPIHC outperforms the existing state-of-the-art EPI prediction methods on the benchmark datasets and chromosome-split datasets, and the study reveal that the communicative learning module can bring explicit information about EPIs, which is ignore by CNN. Moreover, we consider two strategies to improve performances of EPIHC in the cross-cell line prediction, and experimental results show that EPIHC constructed on training cell lines exhibit improved performances for the other cell lines.