An iteration method for identifying yeast essential proteins from heterogeneous network

• Published in: BMC bioinformatics Vol. 20; no. 1; pp. 355 - 13
• Main Authors: Zhao, Bihai, Zhao, Yulin, Zhang, Xiaoxia, Zhang, Zhihong, Zhang, Fan, Wang, Lei
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 24.06.2019; BioMed Central; BMC
• Subjects: Algorithms; Analysis; Chemical properties; Computational biology; Diseases; Essential proteins; Heterogeneous network; Methods; Network architectures; Novels; Protein Domains; Protein Interaction Mapping - methods; Protein Interaction Maps; Protein-protein interaction; Protein-protein interactions; Proteins; Saccharomyces cerevisiae; Saccharomyces cerevisiae - metabolism; Saccharomyces cerevisiae Proteins - chemistry; Saccharomyces cerevisiae Proteins - metabolism; China; Heterogeneous network; Protein-protein interaction; Essential proteins
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-019-2930-2

Essential proteins are distinctly important for an organism's survival and development and crucial to disease analysis and drug design as well. Large-scale protein-protein interaction (PPI) data sets exist in Saccharomyces cerevisiae, which provides us with a valuable opportunity to predict identify essential proteins from PPI networks. Many network topology-based computational methods have been designed to detect essential proteins. However, these methods are limited by the completeness of available PPI data. To break out of these restraints, some computational methods have been proposed by integrating PPI networks and multi-source biological data. Despite the progress in the research of multiple data fusion, it is still challenging to improve the prediction accuracy of the computational methods. In this paper, we design a novel iterative model for essential proteins prediction, named Randomly Walking in the Heterogeneous Network (RWHN). In RWHN, a weighted protein-protein interaction network and a domain-domain association network are constructed according to the original PPI network and the known protein-domain association network, firstly. And then, we establish a new heterogeneous matrix by combining the two constructed networks with the protein-domain association network. Based on the heterogeneous matrix, a transition probability matrix is established by normalized operation. Finally, an improved PageRank algorithm is adopted on the heterogeneous network for essential proteins prediction. In order to eliminate the influence of the false negative, information on orthologous proteins and the subcellular localization information of proteins are integrated to initialize the score vector of proteins. In RWHN, the topology, conservative and functional features of essential proteins are all taken into account in the prediction process. The experimental results show that RWHN obviously exceeds in predicting essential proteins ten other competing methods. We demonstrated that integrating multi-source data into a heterogeneous network can preserve the complex relationship among multiple biological data and improve the prediction accuracy of essential proteins. RWHN, our proposed method, is effective for the prediction of essential proteins.