Computer Science ›› 2017, Vol. 44 ›› Issue (10): 38-44.doi: 10.11896/j.issn.1002-137X.2017.10.007

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Research on Essential Protein Identification Method Based on Improved PSO Algorithm

HONG Hai-yan and LIU Wei   

  • Online:2018-12-01 Published:2018-12-01

Abstract: The essential protein is the most important material basis for the maintenance of all life activities in the living body.With the development of high throughput technology,how to identify the essential proteins from the protein interaction network has become a hot research topic in proteomics.For most of the existing methods are only based on the information of network topology for recognition as well as high false positive of protein-protein interaction data,this paper presented the improved particle swarm algorithm to identify the essential proteins.We considered the network topology characteristics and multi-source biological attribute information to construct the high quality of the weighted networks.We also considered node links between protein to measure the essentiality of protein,and expanded the local network topology to the second-order neighbor,improving the accuracy greatly.We proposed a measure of the overall top-pindex,which reduces the computational complexity.The experimental results on standard data sets show that our algorithm is superior to other algorithms in comparison with other classical algorithms,which can identify more proteins with higher accuracy.

Key words: Essential protein,PSO,PPI

[1] WINZELER E A,ASTROMOFF A,LIANG H,et al.Functionalcharacterization of the S.cerevisiae genome by gene deletion and parallel analysis[J].Science,1999,5(5429):901-906.
[2] CLATWORTHY A E,PIERSON E,HUNG D T.Targeting vi-rulence:a new paradigm for antimicrobial therapy[J].China Ani-mal Husbandry & Veterinary Medicine,2007,3(9):541-548.
[3] GIAEVER G,CHU A M,NI L,et al.Functional profiling of the Saccharomyces cerevisiae genome[J].Nature,2002,418(6896):387-391.
[4] CULLEN LM,ARNDT G M.Genome-wide screening for gene function using RNAi in mammalian cells[J].Immunology & Cell Biology,2005,3(3):217-223.
[5] ROEMER T,JIANG B,DAVISON J,et al.Large-scale essential gene identification in Candida albicans and applications to antifungal drug discovery[J].Molecular Microbiology,2003,0 (1):167-181.
[6] JEONG H,MASON S P,BARABSI A L,et al.Lethality and centrality in protein networks[J].Nature,2001,411(6833):41-42.
[7] HAHN M W,KERN A D.Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks[J].Molecular Biology & Evolution,2005,22(4):803-806.
[8] BATADA N N,HURST L D,TYERS M.Evolutionary andphysiological importance of hub proteins[J].Plos Computational Biology,2006,2(7):e88.
[9] VALLABHAJOSYULA R R,CHAKRAVARTI D,LUTFEALI S,et al.Identifying hubs in protein interaction networks[J].PLoS One,2009,4(4):e5344.
[10] ESTRADE E.Virtual identification of essential proteins within the protein interaction network of yeast[J].Proteomics,2006,6(1):35-40.
[11] FREEMAN L C.A set of measures of centrality based on betweenness[J].Sociometry,1977,40(1):35-41.
[12] WUCHTY S,STADLER P F.Centers of complex networks[J].Journal of Theoretical Biology,2003,3(1):45-53.
[13] ESTRAD E,RODRGUEZ-VELZQUEZ J A.Subgraph centrality in complex networks[J].Phys.Rev.E Stat.Nonlin.& Soft.Matter.Phys.,2005,71(2):056103.
[14] BONACICH P.Power and centrality:a family of measures[J].American Journal of Sociology,1987,2(5):1170-1182.
[15] STEPHENSON K,ZELEN M.Rethinking centrality:methodsand examples[J].Social Networks,1989,1(1):1-37.
[16] LI M,WANG J,CHEN X,et al.A local average connectivity-based method for identifying essential proteins from the network level[J].Computational Biology & Chemistry,2011,5(3):143.
[17] WANG J,LI M,WANG H,et al.Identification of essential proteins based on edge clustering coefficient[J].IEEE/ACM Transactions on Computational Biology & Bioinformatics,2012,9(4):1070.
[18] LI M,WANG J,WANG H,et al.Essential proteins discovery from weighted protein interaction networks[J].Bioinformatics Research & Applications,2010,6053(3):89-100.
[19] HE X,ZHANG J.Why do hubs tend to be essential in protein networks?[J].PLoS Genet,2006,2(6):826-834.
[20] ZOTENKO E,MESTRE J,O’LEARY D P,et al.Why do hubs in the yeast protein interaction network tend to be essential:reexamining the connection between the network topology and essentiality[J].Plos Computational biology,2008,4(8):e1000140..
[21]CHU A H N, TEW K L, LI X L, et al. A unified scoring scheme for detecting essential proteins in protein interaction networks [C]//Proceedings of the 2008 20th IEEE International Confe-rence on Tools with Artificial IntelligenceCICTAI'08). USA: IEEE Computer Society, 2008: 66-73.
[22]LI M,ZHANG H,WANG J X,et al.A new essential protein discovery method based on the integration of protein-protein in-teraction and gene expression data[J].BMC Systems Biology, 2012,6(1): 15.
[23] ZHANG X,XU J,XIAO W X.A new method for the discovery of essential proteins[J].PloS One,2013,8(3):e58763.
[24] LUO J,MA L.A new integration-centric algorithm of identifying essential proteins based on topology structure of protein-protein interaction network and complex information[J].Current Bioinformatics,2013,8(3):380-385.
[25] LI M,ZHENG R,ZHANG H,et al.Effective identification ofessential proteins based on priori knowledge,network topology and gene expressions[J].Methods,2014,67(3):325-333.
[26] JIANG Y,WANG Y,PANG W,et al.Essential protein identification based on essential protein-protein interaction prediction by Integrated Edge Weights[J].Methods,2015,83:51-62.
[27] http://dip.doe-mbi.ucla.edu/dip/Download.cgi?SM=7.
[28] http://www.ncbi.nlm.nih.gov/geo.
[29] TU B P,KUDLICKI A,ROWICKA M,et al.Logic of the Yeast Metabolic Cycle:Temporal Compartmentalization of Cellular Processes[J].Science,2005,0:1152-1158.
[30] ASHBURNER M,BALL C A,BLAKE J A,et al.Gene ontology:tool for the unification of biology.The Gene Ontology Consortium[J].Nat.Genet.,2000,5(1):25-29.
[31] YELLABOINA S,TASNEEM A,ZAYKIN D V,et al.DO-MINE:a comprehensive collection of known and predicted domain-domain interactions[J].Nacleic Acids Res.,2011,9(supp_1):730-735.
[32] O’BRIEN K P,REMM M,SPMMHAMMER E L.Inparanoid:a comprehensive database of eukaryotic orthologs[J].Nucleic Acids Res.,2005,3:D476-480.
[33] MMEWES H W,AMID C,ARNOLD R,et al. MIPS:analysis and annotation of proteins from whole genomes [J]. Nucleic Acids Res. ,2004,32(Suppl l) :41-44.
[34]CHERRY J M, ADLER C, BALL C, et al. SGD: Saccharomyces genome database[J]. Nucleic Acids Res. ,1998,26(1): 73-79.
[35]ZHANG R,LIN Y. DEG 5. O,a database of essential genes in both prokaryotes and eukaryotes[J].Nucleic Acids Res. ,2009, 37 (Suppl. 1): D455-D458.
[36]http://www. sequence. stanford. edu/group.
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