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Volumn 110, Issue 26, 2013, Pages 10872-10877

Optimization criteria and biological process enrichment in homologous multiprotein modules

Author keywords

[No Author keywords available]

Indexed keywords

MULTIPROTEIN COMPLEX;

EID: 84879520199     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1308621110     Document Type: Article
Times cited : (5)

References (43)
  • 1
    • 0141593601 scopus 로고    scopus 로고
    • Conserved pathways within bacteria and yeast as revealed by global protein network alignment
    • Kelley BP, et al. (2003) Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc Natl Acad Sci USA 100(20):11394-11399.
    • (2003) Proc Natl Acad Sci USA , vol.100 , Issue.20 , pp. 11394-11399
    • Kelley, B.P.1
  • 2
    • 13844314048 scopus 로고    scopus 로고
    • Conserved patterns of protein interaction in multiple species
    • Sharan R, et al. (2005) Conserved patterns of protein interaction in multiple species. Proc Natl Acad Sci USA 102(6):1974-1979.
    • (2005) Proc Natl Acad Sci USA , vol.102 , Issue.6 , pp. 1974-1979
    • Sharan, R.1
  • 3
    • 33645985807 scopus 로고    scopus 로고
    • Pairwise alignment of protein interaction networks
    • Koyutürk M, et al. (2006) Pairwise alignment of protein interaction networks. J Comput Biol 13(2):182-199.
    • (2006) J Comput Biol , vol.13 , Issue.2 , pp. 182-199
    • Koyutürk, M.1
  • 4
    • 34548755675 scopus 로고    scopus 로고
    • Comparing protein interaction networks via a graph match-and-split algorithm
    • Narayanan M, Karp RM (2007) Comparing protein interaction networks via a graph match-and-split algorithm. J Comput Biol 14(7):892-907.
    • (2007) J Comput Biol , vol.14 , Issue.7 , pp. 892-907
    • Narayanan, M.1    Karp, R.M.2
  • 5
    • 84861515900 scopus 로고    scopus 로고
    • Algorithms to detect multiprotein modularity conserved during evolution
    • Hodgkinson L, Karp RM (2012) Algorithms to detect multiprotein modularity conserved during evolution. IEEE/ACM Trans Comput Biol Bioinform 9(4):1046-1058.
    • (2012) IEEE/ACM Trans Comput Biol Bioinform , vol.9 , Issue.4 , pp. 1046-1058
    • Hodgkinson, L.1    Karp, R.M.2
  • 6
    • 84859699831 scopus 로고    scopus 로고
    • The gene ontology: Enhancements for 2011
    • Gene Ontology Consortium
    • Gene Ontology Consortium (2012) The Gene Ontology: Enhancements for 2011. Nucleic Acids Res 40(Database issue):D559-D564.
    • (2012) Nucleic Acids Res , vol.40 , Issue.DATABASE ISSUE
  • 7
    • 12344269924 scopus 로고    scopus 로고
    • GO:TermFinder - Open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
    • Boyle EI, et al. (2004) GO:TermFinder - Open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics 20(18):3710-3715.
    • (2004) Bioinformatics , vol.20 , Issue.18 , pp. 3710-3715
    • Boyle, E.I.1
  • 8
    • 36448946146 scopus 로고    scopus 로고
    • Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysis
    • Grossmann S, Bauer S, Robinson PN, Vingron M (2007) Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysis. Bioinformatics 23(22):3024-3031.
    • (2007) Bioinformatics , vol.23 , Issue.22 , pp. 3024-3031
    • Grossmann, S.1    Bauer, S.2    Robinson, P.N.3    Vingron, M.4
  • 9
    • 47049099111 scopus 로고    scopus 로고
    • Ontologizer 2.0 - A multifunctional tool for GOtermenrichment analysis and data exploration
    • Bauer S, Grossmann S, Vingron M, Robinson PN (2008) Ontologizer 2.0 - A multifunctional tool for GOtermenrichment analysis and data exploration. Bioinformatics 24(14):1650-1651.
    • (2008) Bioinformatics , vol.24 , Issue.14 , pp. 1650-1651
    • Bauer, S.1    Grossmann, S.2    Vingron, M.3    Robinson, P.N.4
  • 11
    • 84898957407 scopus 로고
    • Conductance and the rapid mixing property for Markov chains: The approximation of permanent resolved
    • (ACM, New York)
    • Jerrum M, Sinclair A (1988) Conductance and the rapid mixing property for Markov chains: The approximation of permanent resolved. Proceedings of the twentieth annual ACM symposium on Theory of computing (ACM, New York), pp 235-244.
    • (1988) Proceedings of the Twentieth Annual ACM Symposium on Theory of Computing , pp. 235-244
    • Jerrum, M.1    Sinclair, A.2
  • 12
    • 70449359805 scopus 로고    scopus 로고
    • Finding local communities in protein networks
    • Voevodski K, Teng SH, Xia Y (2009) Finding local communities in protein networks. BMC Bioinformatics 10:297.
    • (2009) BMC Bioinformatics , vol.10 , pp. 297
    • Voevodski, K.1    Teng, S.H.2    Xia, Y.3
  • 13
    • 37649028224 scopus 로고    scopus 로고
    • Finding and evaluating community structure in networks
    • Newman ME, Girvan M (2004) Finding and evaluating community structure in networks. Phys Rev E Stat Nonlin Soft Matter Phys 69(2 Pt 2):026113.
    • (2004) Phys Rev e Stat Nonlin Soft Matter Phys , vol.69 , Issue.2 PART 2 , pp. 026113
    • Newman, M.E.1    Girvan, M.2
  • 14
    • 40449109730 scopus 로고    scopus 로고
    • Consistent dissection of the protein interaction network by combining global and local metrics
    • Wang C, Ding C, Yang Q, Holbrook SR (2007) Consistent dissection of the protein interaction network by combining global and local metrics. Genome Biol 8(12):R271.
    • (2007) Genome Biol , vol.8 , Issue.12
    • Wang, C.1    Ding, C.2    Yang, Q.3    Holbrook, S.R.4
  • 15
    • 84856944883 scopus 로고    scopus 로고
    • An iterative network partition algorithm for accurate identification of dense network modules
    • Sun S, Dong X, Fu Y, Tian W (2012) An iterative network partition algorithm for accurate identification of dense network modules. Nucleic Acids Res 40(3):e18.
    • (2012) Nucleic Acids Res , vol.40 , Issue.3
    • Sun, S.1    Dong, X.2    Fu, Y.3    Tian, W.4
  • 17
    • 80052036327 scopus 로고    scopus 로고
    • Biological interaction networks are conserved at the module level
    • Zinman GE, Zhong S, Bar-Joseph Z (2011) Biological interaction networks are conserved at the module level. BMC Syst Biol 5:134.
    • (2011) BMC Syst Biol , vol.5 , pp. 134
    • Zinman, G.E.1    Zhong, S.2    Bar-Joseph, Z.3
  • 18
    • 33847249901 scopus 로고    scopus 로고
    • Specificity and evolvability in eukaryotic protein interaction networks
    • Beltrao P, Serrano L (2007) Specificity and evolvability in eukaryotic protein interaction networks. PLOS Comput Biol 3(2):e25.
    • (2007) PLOS Comput Biol , vol.3 , Issue.2
    • Beltrao, P.1    Serrano, L.2
  • 19
    • 33644617753 scopus 로고    scopus 로고
    • Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets
    • Gandhi TKB, et al. (2006) Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet 38(3):285-293.
    • (2006) Nat Genet , vol.38 , Issue.3 , pp. 285-293
    • Gandhi, T.K.B.1
  • 20
    • 0035211290 scopus 로고    scopus 로고
    • Identification of potential interaction networks using sequence- based searches for conserved protein-protein interactions or "interologs"
    • Matthews LR, et al. (2001) Identification of potential interaction networks using sequence- based searches for conserved protein-protein interactions or "interologs" Genome Res 11(12):2120-2126.
    • (2001) Genome Res , vol.11 , Issue.12 , pp. 2120-2126
    • Matthews, L.R.1
  • 21
    • 75949120438 scopus 로고    scopus 로고
    • How and when should interactome-derived clusters be used to predict functional modules and protein function?
    • Song J, Singh M (2009) How and when should interactome-derived clusters be used to predict functional modules and protein function? Bioinformatics 25(23):3143-3150.
    • (2009) Bioinformatics , vol.25 , Issue.23 , pp. 3143-3150
    • Song, J.1    Singh, M.2
  • 23
    • 54949127160 scopus 로고    scopus 로고
    • IRefIndex: A consolidated protein interaction database with provenance
    • Razick S, Magklaras G, Donaldson IM (2008) iRefIndex: A consolidated protein interaction database with provenance. BMC Bioinformatics 9:405.
    • (2008) BMC Bioinformatics , vol.9 , pp. 405
    • Razick, S.1    Magklaras, G.2    Donaldson, I.M.3
  • 24
    • 79959846617 scopus 로고    scopus 로고
    • PSICQUIC and PSISCORE: Accessing and scoring molecular interactions
    • Aranda B, et al. (2011) PSICQUIC and PSISCORE: Accessing and scoring molecular interactions. Nat Methods 8(7):528-529.
    • (2011) Nat Methods , vol.8 , Issue.7 , pp. 528-529
    • Aranda, B.1
  • 25
    • 84859204939 scopus 로고    scopus 로고
    • The IntAct molecular interaction database in 2012
    • Kerrien S, et al. (2012) The IntAct molecular interaction database in 2012. Nucleic Acids Res 40(Database issue):D841-D846.
    • (2012) Nucleic Acids Res , vol.40 , Issue.DATABASE ISSUE
    • Kerrien, S.1
  • 26
    • 78651328883 scopus 로고    scopus 로고
    • The BioGRID interaction database: 2011 update
    • Stark C, et al. (2011) The BioGRID interaction database: 2011 update. Nucleic Acids Res 39(Database issue):D698-D704.
    • (2011) Nucleic Acids Res , vol.39 , Issue.DATABASE ISSUE
    • Stark, C.1
  • 27
    • 0347755535 scopus 로고    scopus 로고
    • The database of interacting proteins: 2004 update
    • Salwinski L, et al. (2004) The database of interacting proteins: 2004 update. Nucleic Acids Res 32(Database issue):D449-D451.
    • (2004) Nucleic Acids Res , vol.32 , Issue.DATABASE ISSUE
    • Salwinski, L.1
  • 28
    • 58149193222 scopus 로고    scopus 로고
    • Human Protein Reference Database - 2009 update
    • Keshava Prasad TS, et al. (2009) Human Protein Reference Database - 2009 update. Nucleic Acids Res 37(Database issue):D767-D772.
    • (2009) Nucleic Acids Res , vol.37 , Issue.DATABASE ISSUE
    • Keshava Prasad, T.S.1
  • 29
    • 79955667824 scopus 로고    scopus 로고
    • The biomolecular interaction network database in PSI-MI 2.5
    • Isserlin R, El-Badrawi RA, Bader GD (2011) The Biomolecular Interaction Network Database in PSI-MI 2.5. Database (Oxford) 2011:baq037.
    • (2011) Database (Oxford) , vol.2011
    • Isserlin, R.1    El-Badrawi, R.A.2    Bader, G.D.3
  • 30
    • 84860918589 scopus 로고    scopus 로고
    • MINT, the molecular interaction database: 2012 update
    • Licata L, et al. (2012) MINT, the molecular interaction database: 2012 update. Nucleic Acids Res 40(Database issue):D857-D861.
    • (2012) Nucleic Acids Res , vol.40 , Issue.DATABASE ISSUE
    • Licata, L.1
  • 31
    • 78651331299 scopus 로고    scopus 로고
    • MIPS: Curated databases and comprehensive secondary data resources in 2010
    • Mewes HW, et al. (2011) MIPS: Curated databases and comprehensive secondary data resources in 2010. Nucleic Acids Res 39(Database issue):D220-D224.
    • (2011) Nucleic Acids Res , vol.39 , Issue.DATABASE ISSUE
    • Mewes, H.W.1
  • 32
    • 51049113607 scopus 로고    scopus 로고
    • InnateDB: Facilitating systems-level analyses of the mammalian innate immune response
    • Lynn DJ, et al. (2008) InnateDB: Facilitating systems-level analyses of the mammalian innate immune response. Mol Syst Biol 4:218.
    • (2008) Mol Syst Biol , vol.4 , pp. 218
    • Lynn, D.J.1
  • 34
    • 84860833500 scopus 로고    scopus 로고
    • Reorganizing the protein space at the Universal Protein Resource (UniProt)
    • UniProt Consortium
    • UniProt Consortium (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res 40(Database issue):D71-D75.
    • (2012) Nucleic Acids Res , vol.40 , Issue.DATABASE ISSUE
  • 35
    • 84857745267 scopus 로고    scopus 로고
    • Detabase resources of the National Center for Biotechnology Information
    • Sayers EW, et al. (2012) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 40(Database issue):D13-D25.
    • (2012) Nucleic Acids Res , vol.40 , Issue.DATABASE ISSUE
    • Sayers, E.W.1
  • 36
    • 35448974490 scopus 로고    scopus 로고
    • Fossils and phylogenies: Integrating multiple lines of evidence to investigate the origin of early major metazoan lineages
    • Cartwright P, Collins A (2007) Fossils and phylogenies: Integrating multiple lines of evidence to investigate the origin of early major metazoan lineages. Integr Comp Biol 47(5): 744-751.
    • (2007) Integr Comp Biol , vol.47 , Issue.5 , pp. 744-751
    • Cartwright, P.1    Collins, A.2
  • 37
    • 80053278126 scopus 로고    scopus 로고
    • Eukaryotic genome complexity
    • Pray LA (2008) Eukaryotic genome complexity. Nature Education. Available online at http://www.nature.com/scitable/topicpage/eukaryotic-genome-complexity- 437.
    • (2008) Nature Education
    • Pray, L.A.1
  • 39
    • 84863304598 scopus 로고    scopus 로고
    • R Development Core Team (R Foundation for Statistical Computing, Vienna)
    • R Development Core Team (2012) R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, Vienna).
    • (2012) R: A Language and Environment for Statistical Computing
  • 41
    • 33750228994 scopus 로고    scopus 로고
    • Relative importance for linear regression in R: The package relaimpo
    • Groemping U (2006) Relative importance for linear regression in R: The package relaimpo. J Stat Softw 17(1):17.
    • (2006) J Stat Softw , vol.17 , Issue.1 , pp. 17
    • Groemping, U.1
  • 42
    • 34248397223 scopus 로고    scopus 로고
    • Estimators of relative importance in linear regression based on variance decomposition
    • Groemping U (2007) Estimators of relative importance in linear regression based on variance decomposition. Am Stat 61(2):139-147.
    • (2007) Am Stat , vol.61 , Issue.2 , pp. 139-147
    • Groemping, U.1
  • 43
    • 0032439915 scopus 로고    scopus 로고
    • On variable importance in linear regression
    • Thomas DR, Hughes E, Zumbo BD (1998) On variable importance in linear regression. Soc Indic Res 45(1-3):253-275.
    • (1998) Soc Indic Res , vol.45 , Issue.1-3 , pp. 253-275
    • Thomas, D.R.1    Hughes, E.2    Zumbo, B.D.3


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