DWPPI: A Deep Learning Approach for Predicting Protein–Protein Interactions in Plants Based on Multi-Source Information With a Large-Scale Biological Network

Frontiers in Bioengineering and Biotechnology

Li-Ping Li¹  Zheng-Yang Zhao²  Wen-Zhun Huang²  Zhu-Hong You²  Jian-Xin Guo²  Jie Pan²  Li-Ping Wang²  Chang-Qing Yu² 

[1] College of Grassland and Environment Science, Xinjiang Agricultural University, Urumqi, China;School of Information Engineering, Xijing University, Xi’an, China;

关键词: plant;    protein-protein interaction;    network embedding;    multi-source information;    deep neural networks;   

DOI  :  10.3389/fbioe.2022.807522

来源: DOAJ

【 摘 要 】

The prediction of protein–protein interactions (PPIs) in plants is vital for probing the cell function. Although multiple high-throughput approaches in the biological domain have been developed to identify PPIs, with the increasing complexity of PPI network, these methods fall into laborious and time-consuming situations. Thus, it is essential to develop an effective and feasible computational method for the prediction of PPIs in plants. In this study, we present a network embedding-based method, called DWPPI, for predicting the interactions between different plant proteins based on multi-source information and combined with deep neural networks (DNN). The DWPPI model fuses the protein natural language sequence information (attribute information) and protein behavior information to represent plant proteins as feature vectors and finally sends these features to a deep learning–based classifier for prediction. To validate the prediction performance of DWPPI, we performed it on three model plant datasets: Arabidopsis thaliana (A. thaliana), mazie (Zea mays), and rice (Oryza sativa). The experimental results with the fivefold cross-validation technique demonstrated that DWPPI obtains great performance with the AUC (area under ROC curves) values of 0.9548, 0.9867, and 0.9213, respectively. To further verify the predictive capacity of DWPPI, we compared it with some different state-of-the-art machine learning classifiers. Moreover, case studies were performed with the AC149810.2_FGP003 protein. As a result, 14 of the top 20 PPI pairs identified by DWPPI with the highest scores were confirmed by the literature. These excellent results suggest that the DWPPI model can act as a promising tool for related plant molecular biology.

【 授权许可】

Unknown