title: Identifying the hub proteins from complicated membrane protein network systems.
abstract: The so-called "hub proteins" are those proteins in a protein-protein interaction network system that have remarkably higher interaction relations (or degrees) than the others. Therefore, the information of hub proteins can provide very useful insights for selecting or prioritizing targets during drug development. In this paper, by combining the multi-agent-based method with the graphical spectrum analysis and immune-genetic algorithm, a novel simulator for identifying the hub proteins from membrane protein interaction networks is proposed. As a demonstration of using the simulator, two hub membrane proteins, YPL227C and YIL147C, were identified from a complicated network system consisting of 1500 membrane proteins. Meanwhile, along with the two identified hub proteins, their molecular functions, biological processes, and cellular components were also revealed. It is anticipated that the hub-protein-simulator may become a very useful tool for system biology and drug development, particularly in deciphering unknown protein functions, determining protein complexes, and in identifying the key targets from a complicated disease system.
authors.affiliation: Dean of College of Information Sciences and Technology, Donghua University, Shanghai 201620, China. ysding@dhu.edu.cn
authors.forename: Yi-Zhen
authors.initials: YZ
authors.lastname: Shen
authors.forename: Yong-Sheng
authors.initials: YS
authors.lastname: Ding
authors.forename: Quan
authors.initials: Q
authors.lastname: Gu
authors.forename: Kuo-Chen
authors.initials: KC
authors.lastname: Chou
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D047908:Intracellular Signaling Peptides and Proteins / Q000737:chemistry*; D008565:Membrane Proteins / Q000737:chemistry*; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D011494:Protein Kinases / Q000737:chemistry*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry*
chemical_list: D047908:Intracellular Signaling Peptides and Proteins; D008565:Membrane Proteins; D029701:Saccharomyces cerevisiae Proteins; D011494:Protein Kinases; C083749:SLN1 protein, S cerevisiae