NDLI: An Iteration Method for Identifying Yeast Essential Proteins From Weighted PPI Network Based on Topological and Functional Features of Proteins

Content Provider	Directory of Open Access Journals (DOAJ)
Author	Shiyuan Li Zhiping Chen Xin He Zhen Zhang Tingrui Pei Yihong Tan Lei Wang
Abstract	Accumulating studies have indicated that essential proteins play critical roles in numerous biological processes. With the rapid development of high-throughput technologies, a large number of Protein-Protein Interaction (PPI) data have been found in Saccharomyces cerevisiae, which facilitate the formation of PPI networks. Up to now, a series of computational methods for predicting essential proteins from PPI networks have been proposed successively. However, the prediction accuracy of these computational methods is still not quite satisfactory. In this paper, a novel prediction method called CVIM is proposed to infer potential essential proteins. In CVIM, original PPI networks will be first transferred into weighted PPI networks by implementing PCC (Pearson Correlation Coefficient) on protein gene expression data. And then, based on weighted PPI networks and information of orthologous proteins, some critical network topological features and protein functional features will be extracted for each protein in the weighted PPI network. Finally, based on these newly extracted topological and functional features of proteins, an iterative algorithm will be designed to predict essential proteins. In order to evaluate the identification performance of CVIM, we have compared CVIM with 13 kinds of state-of-the-art prediction methods. Experimental results show that CVIM can achieve prediction accuracies of 92%, 80% and 71% out of the top 1%, 5% and 10% candidate proteins separately, which significantly outperform the prediction accuracies achieved by those state-of-the-art prediction methods. We have demonstrated that the prediction accuracy of essential proteins can be effectively improved by integrating the functional and network topological characteristics of proteins, which means that the novel method CVIM may be an excellent addition to the protein researches in the future.
e-ISSN	21693536
DOI	10.1109/ACCESS.2020.2993860
Journal	IEEE Access
Volume Number	8
Language	English
Publisher	IEEE
Publisher Date	2020-01-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Electrical Engineering. Electronics. Nuclear Engineering Characteristic Vector Orthologous Proteins Essential Proteins Weighted Protein-protein Interaction Network Iteration Method
Content Type	Text
Resource Type	Article

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