Protein complex prediction in interaction network based on network motif. (December 2020)

• Record Type: Journal Article
• Authors: Patra, Sabyasachi; Mohapatra, Anjali
• Is Part Of: Computational biology and chemistry. Volume 89(2020)
• Publication Date: 2020-12
• Subjects: Biological network -- Network motif -- Feature matrix -- Feature normalization -- Protein complex -- Neighborhood search; Chemistry -- Data processing -- Periodicals; Biology -- Data processing -- Periodicals; Biochemistry -- Data processing; Biology -- Data processing; Molecular biology -- Data processing; Periodicals; Electronic journals; 542.85
• DOI: 10.1016/j.compbiolchem.2020.107399
• Languages: English
• ISSNs: 1476-9271

Abstract

Abstract: The enormous size of Protein–Protein Interaction (PPI) networks demands efficient computational methods to extract biologically significant protein complexes. A wide variety of algorithms have been proposed to predict protein complexes from PPI networks. However, it is still a challenging task to detect protein complexes with high accuracy and manageable sensitivity. In this manuscript, a novel complex prediction algorithm based on Network Motif (CPNM) is proposed. This algorithm addresses the role of proteins in the embeddings of network motif. These roles are used to define feature vectors and feature weights of proteins. Based on these features, a neighborhood search technique predict the protein complexes that consider both the inherent organization of proteins as well as the dense regions in PPI networks. The performance of the proposed algorithm is evaluated using various evaluation metrics like Precision, Recall, F -measure, Sensitivity, PPV, and Accuracy. The research finding indicates that the proposed algorithm outperforms most of the competing algorithms like MCODE, DPClus, RNSC, COACH, ClusterONE, CMC and PROCODE over the PPI network of Saccharomyces cerevisiae and Homo sapiens .