title: A New Method for Identifying Essential Proteins Based on Network Topology Properties and Protein Complexes.
abstract: Essential proteins are indispensable to the viability and reproduction of an organism. The identification of essential proteins is necessary not only for understanding the molecular mechanisms of cellular life but also for disease diagnosis, medical treatments and drug design. Many computational methods have been proposed for discovering essential proteins, but the precision of the prediction of essential proteins remains to be improved. In this paper, we propose a new method, LBCC, which is based on the combination of local density, betweenness centrality (BC) and in-degree centrality of complex (IDC). First, we introduce the common centrality measures; second, we propose the densities Den1(v) and Den2(v) of a node v to describe its local properties in the network; and finally, the combined strategy of Den1, Den2, BC and IDC is developed to improve the prediction precision. The experimental results demonstrate that LBCC outperforms traditional topological measures for predicting essential proteins, including degree centrality (DC), BC, subgraph centrality (SC), eigenvector centrality (EC), network centrality (NC), and the local average connectivity-based method (LAC). LBCC also improves the prediction precision by approximately 10 percent on the YMIPS and YMBD datasets compared to the most recently developed method, LIDC.
authors.affiliation: Beijing Key Lab of Traffic Data Analysis and Mining, Beijing Jiaotong University, Beijing, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Qin
authors.affiliation: Beijing Key Lab of Traffic Data Analysis and Mining, Beijing Jiaotong University, Beijing, China.
authors.forename: Yongqi
authors.initials: Y
authors.lastname: Sun
authors.affiliation: Beijing Key Lab of Traffic Data Analysis and Mining, Beijing Jiaotong University, Beijing, China.
authors.forename: Yadong
authors.initials: Y
authors.lastname: Dong
mesh_terms: D019295:Computational Biology; D025941:Protein Interaction Mapping / Q000379:methods*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*; D013223:Statistics as Topic
chemical_list: D029701:Saccharomyces cerevisiae Proteins