基于改进的PSO算法的关键蛋白质识别方法研究

doi:10.11896/j.issn.1002-137X.2017.10.007

摘要/Abstract

摘要： 关键蛋白质是生物体内维持所有生命活动最重要的物质基础。随着高通量技术的发展,如何从蛋白质相互作用网络中识别出关键蛋白质成为目前蛋白质组学的研究热点。针对大部分现有方法仅仅基于网络拓扑结构信息进行识别以及蛋白质相互作用数据假阳性高的问题,提出了改进的粒子群算法来识别关键蛋白质。通过综合考虑网络拓扑结构特性和多源生物属性信息构建了高质量的加权网络,还考虑使用蛋白质节点间联系的紧密程度来衡量蛋白质的关键性,并扩展局部网络拓扑至二阶邻居,大大提高了预测的准确率。提出了衡量top-p关键蛋白质的整体性指标,降低了计算复杂度。在标准数据集上的实验结果表明,与其他经典算法相比,所提算法更具优势,能够识别出更多的蛋白质,具有较高的准确率。

关键词: 关键蛋白质,PSO,蛋白质相互作用网络

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

洪海燕,刘维. 基于改进的PSO算法的关键蛋白质识别方法研究[J]. 计算机科学, 2017, 44(10): 38-44. https://doi.org/10.11896/j.issn.1002-137X.2017.10.007

HONG Hai-yan and LIU Wei. Research on Essential Protein Identification Method Based on Improved PSO Algorithm[J]. Computer Science, 2017, 44(10): 38-44. https://doi.org/10.11896/j.issn.1002-137X.2017.10.007

参考文献

[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.

Metrics

Viewed

Full text

Abstract

Cited

Shared

Discussed