全部 标题 作者
关键词 摘要

OALib Journal期刊
ISSN: 2333-9721
费用:99美元

查看量下载量

相关文章

更多...
电子学报  2014 

基于多视图融合的蛋白质功能模块检测方法

DOI: 10.3969/j.issn.0372-2112.2014.12.001, PP. 2337-2344

Keywords: 蛋白质相互作用网络,网络模块挖掘,多数据集成,可重叠聚类

Full-Text   Cite this paper   Add to My Lib

Abstract:

结合多种生物数据分析蛋白质相互作用网络(Protein-ProteinInteractionNetwork,PPIN)中的功能模块结构,是目前蛋白质功能计算分析领域亟待解决的难题之一.本文提出了一种基于聚合非负矩阵分解(CollectiveNon-negativeMatrixFactorization,CoNMF)的多视图一致性功能模块检测方法,该方法同时逼近多视图数据,寻找统一的最优解达到对原多数据的最优近似.根据该统一解得到功能模块关系,同时该方法能够找到可重叠性的功能模块.实验结果显示本文所提出算法通过融合基因本体、基因表达谱与PPIN数据,在模块检测准确度上有一定提高,检测出的蛋白质功能模块具有真实生物意义.

References

[1]  Bonetta L.Protein-protein interactions:Interactome under construction[J].Nature,2010,468(7325):851-854.
[2]  Bader GD,Hogue CW.An automated method for finding molecular complexes in large protein interaction networks[J/OL].BMC Bioinformatics,2003,4.http://www.ncbi.nlm.nih.gov/pmc/articles/PMC149346/pdf/1471-2105-4-2.pdf,2003-01-13/2013-11-19.
[3]  Young-Rae C,Woochang H,Aidong Z.Efficient modularization of weighted protein interaction networks using k-hop graph reduction[A].Bioinformatics and Bioengineering,2006 BIBE 2006 Sixth IEEE Symposium on[C].Virginia:IEEE,2006.289-98.
[4]  Ulitsky I,Shamir R.Identifying functional modules using expression profiles and confidence-scored protein interactions[J].Bioinformatics,2009,25(9):1158-1164.
[5]  Sprinzak E,Sattath S,Margalit H.How reliable are experimental protein-protein interaction data[J].Journal of Molecular Biology,2003,327(5):919-923.
[6]  Adamcsek B,Palla G,Farkas IJ,Derenyi I,Vicsek T.CFinder:locating cliques and overlapping modules in biological networks[J].Bioinformatics,2006,22(8):1021-1023.
[7]  Oti M,Brunner HG.The modular nature of genetic diseases[J].Clincal Genetics,2007,71(1):1-11.
[8]  Chen J,Yuan B.Detecting functional modules in the yeast protein protein interaction network[J].Bioinformatics,2006,22(18):2283-2290.
[9]  Segal E,Wang H,Koller D.Discovering molecular pathways from protein interaction and gene expression data[J].Bioinformatics,2003,19(suppl 1):i264-i272.
[10]  Li M,Wu XH,Wang JX,Pan Y.Towards the identification of protein complexes and functional modules by integrating PPI network and gene expression data[J/OL].BMC Bioinformatics,2012,13.http://www.biomedcentral.com/content/pdf/1471-2105-13-109.pdf,2012-05-23/2013-11-19.
[11]  Young-Rae C,Lei S,Aidong Z.FlowNet:flow-based approach for efficient analysis of complex biological networks[A]. Data Mining,2009 ICDM ''09 Ninth IEEE International Conference on[C].Florida:IEEE,2009.91-100.
[12]  Consortium GO.The Gene Ontology (GO) database and informatics resource[J].Nucleic Acids Research,2004,32(suppl 1):D258-D261.
[13]  du Plessis L,Skunca N,Dessimoz C.The what,where,how and why of gene ontology-a primer for bioinformaticians[J].Briefings in Bioinformatics,2011,12(6):723-735.
[14]  von Luxburg U.A tutorial on spectral clustering[J].Statistics and Computing,2007,17(4):395-416.
[15]  Smola AJ,Kondor R.Kernels and regularization on graphs[J].Learning Theory and Kernel Machines,2003,2777:144-158.
[16]  Strehl A,Ghosh J.Cluster ensembles—a knowledge reuse framework for combining multiple partitions[J].J Mach Learn Res,2003,3(1):583-617.
[17]  Fern XZ,Brodley CE.Solving cluster ensemble problems by bipartite graph partitioning[A].Proceedings of the Twenty-first International Conference on Machine Learning[C].New York:ACM,2004.36-45.
[18]  Gavin A-C.Proteome survey reveals modularity of the yeast cell machinery[J].Nature,2006,440(30):631-636.
[19]  Rhee SY,Wood V,Dolinski K,Draghici S.Use and misuse of the gene ontology annotations[J].Nat Rev Genet,2008,9(7):509-515.
[20]  Ding C,Li T,Peng W,Park H.Orthogonal nonnegative matrix t-factorizations for clustering[A].Proceedings of the 12th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining[C].Philadelphia:ACM,2006.126-135.
[21]  Wang H,Huang H,Ding C.Simultaneous clustering of multi-type relational data via symmetric nonnegative matrix tri-factorization[A].Proceedings of the 20th ACM International Conference on Information and Knowledge Management[C].Glasgow:ACM,2011.279-284.
[22]  Kim H,Park H.Nonnegative matrix factorization based on alternating nonnegativity constrained least squares and active set method[J].SIAM Journal on Matrix Analysis and Applications,2008,30(2):713-730.
[23]  Zhang T,Shen R,Lu H.Using non-negative matrix factorization to cluster learners and construct learning communities[J].Chinese Journal of Electronics,2011,20(2):207-211.
[24]  Xu W,Liu X,Gong Y.Document clustering based on non-negative matrix factorization[A].Proceedings of the 26th Annual International ACM SIGIR Conference on Research and Development in Informaion Retrieval[C].New York:ACM,2003.267-273.
[25]  Resnik P.Semantic similarity in a taxonomy:An information-based measure and its application to problems of ambiguity in natural language[J].J Artif Intell Res,1999,11(1):95-130.
[26]  Lin D.An information-theoretic definition of similarity[A].Proceedings of the Fifteenth International Conference on Machine Learning[C].Scotland:Springer,1998.296-304.
[27]  Anderson JB,Sirjusingh C,Syed N,Lafayette S.Gene expression and evolution of antifungal drug resistance[J].Antimicrob Agents Chemother,2009,53(5):1931-1937.
[28]  Pu SY,Wong J,Turner B,Cho E,Wodak SJ.Up-to-date catalogues of yeast protein complexes[J].Nucleic Acids Research,2009,37(3):825-831.
[29]  Jianxin W,Min L,Jianer C,Yi P.A fast hierarchical clustering algorithm for functional modules dscovery in protein interaction networks[J].IEEE/ACM Transactions on Computational Biology and Bioinformatics,2011,8(3):607-620.
[30]  Macropol K,Can T,Singh AK.RRW:Repeated random walks on genome-scale protein networks for local cluster discovery[J/OL].BMC Bioinformatics,2009,10.http://www.biomedcentral.com/content/pdf/1471-2105-10-283.pdf,2009-09-09/2013-11-19.

Full-Text

Contact Us

service@oalib.com

QQ:3279437679

WhatsApp +8615387084133