DeepPBI-KG: a deep learning method for the prediction of phage-bacteria interactions based on key genes

作者：Tongqing Wei, Chenqi Lu, Hanxiao Du, Qianru Yang, Xinru Qi, Yankun Liu, Yi Zhang, Chen Chen, Yutong Li, Yuanhao Tang, Wenhong Zhang, Tao Xu, Ning Jiang · 发表于：Briefings in Bioinformatics · 年份：2024 · DOI：10.1093/bib/bbae484 · 被引用次数：11 · 研究领域：Bacteriophages and microbial interactions、Genomics and Phylogenetic Studies、Plant Virus Research Studies

Phages, the natural predators of bacteria, were discovered more than 100 years ago. However, increasing antimicrobial resistance rates have revitalized phage research. Methods that are more time-consuming and efficient than wet-laboratory experiments are needed to help screen phages quickly for therapeutic use. Traditional computational methods usually ignore the fact that phage-bacteria interactions are achieved by key genes and proteins. Methods for intraspecific prediction are rare since almost all existing methods consider only interactions at the species and genus levels. Moreover, most strains in existing databases contain only partial genome information because whole-genome information for species is difficult to obtain. Here, we propose a new approach for interaction prediction by constructing new features from key genes and proteins via the application of K-means sampling to select high-quality negative samples for prediction. Finally, we develop DeepPBI-KG, a corresponding prediction tool based on feature selection and a deep neural network. The results show that the average area under the curve for prediction reached 0.93 for each strain, and the overall AUC and area under the precision-recall curve reached 0.89 and 0.92, respectively, on the independent test set; these values are greater than those of other existing prediction tools. The forward and reverse validation results indicate that key genes and key proteins regulate and influence the interaction, which su...