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Volumn 8, Issue 9, 2012, Pages

What Evidence Is There for the Homology of Protein-Protein Interactions?

Author keywords

[No Author keywords available]

Indexed keywords

PROTEINS;

EID: 84866928522     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002645     Document Type: Article
Times cited : (36)

References (61)
  • 1
    • 0030660581 scopus 로고    scopus 로고
    • A genomic perspective on protein families
    • Tatusov RL, Koonin EV, Lipman DJ, (1997) A genomic perspective on protein families. Science 278: 631-637.
    • (1997) Science , vol.278 , pp. 631-637
    • Tatusov, R.L.1    Koonin, E.V.2    Lipman, D.J.3
  • 2
    • 80052823795 scopus 로고    scopus 로고
    • Orthology prediction methods: A quality assessment using curated protein families
    • Trachana K, Larsson TA, Powell S, Chen WH, Doerks T, et al. (2011) Orthology prediction methods: A quality assessment using curated protein families. Bioessays 33: 769-780.
    • (2011) Bioessays , vol.33 , pp. 769-780
    • Trachana, K.1    Larsson, T.A.2    Powell, S.3    Chen, W.H.4    Doerks, T.5
  • 4
    • 59949096873 scopus 로고    scopus 로고
    • EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates
    • Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, et al. (2009) EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res 19: 327-335.
    • (2009) Genome Res , vol.19 , pp. 327-335
    • Vilella, A.J.1    Severin, J.2    Ureta-Vidal, A.3    Heng, L.4    Durbin, R.5
  • 5
    • 0034614678 scopus 로고    scopus 로고
    • Protein interaction mapping in C. elegans using proteins involved in vulval development
    • Walhout AJM, Sordella R, Lu X, Hartley JL, Temple GF, et al. (2000) Protein interaction mapping in C. elegans using proteins involved in vulval development. Science 287: 116-122.
    • (2000) Science , vol.287 , pp. 116-122
    • Walhout, A.J.M.1    Sordella, R.2    Lu, X.3    Hartley, J.L.4    Temple, G.F.5
  • 6
    • 10244242604 scopus 로고    scopus 로고
    • POINT: a database for the prediction of protein-protein interactions based on the orthologous interactome
    • Huang TW, Tien AC, Huang WS, Lee YCG, Peng CL, et al. (2004) POINT: a database for the prediction of protein-protein interactions based on the orthologous interactome. Bioinformatics 20: 3273-3276.
    • (2004) Bioinformatics , vol.20 , pp. 3273-3276
    • Huang, T.W.1    Tien, A.C.2    Huang, W.S.3    Lee, Y.C.G.4    Peng, C.L.5
  • 7
    • 9144264169 scopus 로고    scopus 로고
    • A map of the interactome network of the metazoan C. elegans
    • Li S, Armstrong CM, Bertin N, Ge H, Milstein S, et al. (2004) A map of the interactome network of the metazoan C. elegans. Science 303: 540-543.
    • (2004) Science , vol.303 , pp. 540-543
    • Li, S.1    Armstrong, C.M.2    Bertin, N.3    Ge, H.4    Milstein, S.5
  • 8
    • 18744376914 scopus 로고    scopus 로고
    • Online predicted human interaction database
    • Brown KR, Jurisica I, (2005) Online predicted human interaction database. Bioinformatics 21: 2076-2082.
    • (2005) Bioinformatics , vol.21 , pp. 2076-2082
    • Brown, K.R.1    Jurisica, I.2
  • 9
    • 33947312507 scopus 로고    scopus 로고
    • HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms
    • Persico M, Ceol A, Gavrila C, Hoffmann R, Florio A, et al. (2005) HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms. BMC Bioinformatics 6: S21.
    • (2005) BMC Bioinformatics , vol.6
    • Persico, M.1    Ceol, A.2    Gavrila, C.3    Hoffmann, R.4    Florio, A.5
  • 10
    • 30644463216 scopus 로고    scopus 로고
    • Cluster analysis of networks generated through homology: automatic identification of important protein communities involved in cancer metastasis
    • Jonsson P, Cavanna T, Zicha D, Bates P, (2006) Cluster analysis of networks generated through homology: automatic identification of important protein communities involved in cancer metastasis. BMC Bioinformatics 7: 2.
    • (2006) BMC Bioinformatics , vol.7 , pp. 2
    • Jonsson, P.1    Cavanna, T.2    Zicha, D.3    Bates, P.4
  • 11
    • 34548855730 scopus 로고    scopus 로고
    • Unequal evolutionary conservation of human protein interactions in interologous networks
    • Brown K, Jurisica I, (2007) Unequal evolutionary conservation of human protein interactions in interologous networks. Genome Biol 8: R95.
    • (2007) Genome Biol , vol.8
    • Brown, K.1    Jurisica, I.2
  • 12
    • 34250221728 scopus 로고    scopus 로고
    • Reconstruction of human protein interolog network using evolutionary conserved network
    • Huang TW, Lin CY, Kao CY, (2007) Reconstruction of human protein interolog network using evolutionary conserved network. BMC Bioinformatics 8: 152.
    • (2007) BMC Bioinformatics , vol.8 , pp. 152
    • Huang, T.W.1    Lin, C.Y.2    Kao, C.Y.3
  • 14
    • 54549088958 scopus 로고    scopus 로고
    • Prediction of evolutionarily conserved interologs in Mus musculus
    • Yellaboina S, Dudekula D, Ko M, (2008) Prediction of evolutionarily conserved interologs in Mus musculus. BMC Genomics 9: 465.
    • (2008) BMC Genomics , vol.9 , pp. 465
    • Yellaboina, S.1    Dudekula, D.2    Ko, M.3
  • 15
    • 57649203329 scopus 로고    scopus 로고
    • Ortholog-based protein-protein interaction prediction and its application to inter-species interactions
    • Lee SA, Chan Ch, Tsai CH, Lai JM, Wang FS, et al. (2008) Ortholog-based protein-protein interaction prediction and its application to inter-species interactions. BMC Bioinformatics 9: S11.
    • (2008) BMC Bioinformatics , vol.9
    • Lee, S.A.1    Chan, C.2    Tsai, C.H.3    Lai, J.M.4    Wang, F.S.5
  • 16
    • 72549085099 scopus 로고    scopus 로고
    • Phylogeny-guided interaction mapping in seven eukaryotes
    • Dutkowski J, Tiuryn J, (2009) Phylogeny-guided interaction mapping in seven eukaryotes. BMC Bioinformatics 10: 393.
    • (2009) BMC Bioinformatics , vol.10 , pp. 393
    • Dutkowski, J.1    Tiuryn, J.2
  • 17
    • 77950444122 scopus 로고    scopus 로고
    • Building and analyzing protein interactome networks by cross-species comparisons
    • Wiles A, Doderer M, Ruan J, Gu TT, Ravi D, et al. (2010) Building and analyzing protein interactome networks by cross-species comparisons. BMC Syst Bio 4: 36.
    • (2010) BMC Syst Bio , vol.4 , pp. 36
    • Wiles, A.1    Doderer, M.2    Ruan, J.3    Gu, T.T.4    Ravi, D.5
  • 18
    • 79960558700 scopus 로고    scopus 로고
    • Homology::InterologWalk - A Perl module to build putative protein-protein interaction networks through interolog mapping
    • Gallone G, Simpson T, Armstrong J, Jarman A, (2011) Homology::InterologWalk- A Perl module to build putative protein-protein interaction networks through interolog mapping. BMC Bioinformatics 12: 289.
    • (2011) BMC Bioinformatics , vol.12 , pp. 289
    • Gallone, G.1    Simpson, T.2    Armstrong, J.3    Jarman, A.4
  • 19
    • 33644617753 scopus 로고    scopus 로고
    • Analysis of the human protein interactome and comparison with yeast, worm and y interaction datasets
    • Gandhi TKB, Zhong J, Mathivanan S, Karthick L, Chandrika KN, et al. (2006) Analysis of the human protein interactome and comparison with yeast, worm and y interaction datasets. Nat Genet 38: 285-293.
    • (2006) Nat Genet , vol.38 , pp. 285-293
    • Gandhi, T.K.B.1    Zhong, J.2    Mathivanan, S.3    Karthick, L.4    Chandrika, K.N.5
  • 20
    • 79957788300 scopus 로고    scopus 로고
    • Measuring the evolutionary rate of protein-protein interaction
    • Qian W, He X, Chan E, Xu H, Zhang J, (2011) Measuring the evolutionary rate of protein-protein interaction. Proc Natl Acad Sci U S A 108: 8725-8730.
    • (2011) Proc Natl Acad Sci U S A , vol.108 , pp. 8725-8730
    • Qian, W.1    He, X.2    Chan, E.3    Xu, H.4    Zhang, J.5
  • 21
    • 0035211290 scopus 로고    scopus 로고
    • Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or interologs
    • Matthews LR, Vaglio P, Reboul J, Ge H, Davis BP, et al. (2001) Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or interologs. Genome Res 11: 2120-2126.
    • (2001) Genome Res , vol.11 , pp. 2120-2126
    • Matthews, L.R.1    Vaglio, P.2    Reboul, J.3    Ge, H.4    Davis, B.P.5
  • 22
    • 3042569597 scopus 로고    scopus 로고
    • Annotation transfer between genomes: Protein-protein interologs and protein-DNA regulogs
    • Yu H, Luscombe NM, Lu HX, Zhu X, Xia Y, et al. (2004) Annotation transfer between genomes: Protein-protein interologs and protein-DNA regulogs. Genome Res 14: 1107-1118.
    • (2004) Genome Res , vol.14 , pp. 1107-1118
    • Yu, H.1    Luscombe, N.M.2    Lu, H.X.3    Zhu, X.4    Xia, Y.5
  • 23
    • 33746622998 scopus 로고    scopus 로고
    • Protein-protein interactions more conserved within species than across species
    • Mika S, Rost B, (2006) Protein-protein interactions more conserved within species than across species. PLoS Comput Biol 2: e79.
    • (2006) PLoS Comput Biol , vol.2
    • Mika, S.1    Rost, B.2
  • 24
    • 77649299348 scopus 로고    scopus 로고
    • An atlas of combinatorial transcriptional regulation in mouse and man
    • Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, et al. (2010) An atlas of combinatorial transcriptional regulation in mouse and man. Cell 140: 744-752.
    • (2010) Cell , vol.140 , pp. 744-752
    • Ravasi, T.1    Suzuki, H.2    Cannistraci, C.V.3    Katayama, S.4    Bajic, V.B.5
  • 26
    • 0036580169 scopus 로고    scopus 로고
    • Protein interactions: Two methods for assessment of the reliability of high-throughput observations
    • Deane CM, Salwiski L, Xenarios I, Eisenberg D, (2002) Protein interactions: Two methods for assessment of the reliability of high-throughput observations. Mol Cell Proteomics 1: 349-356.
    • (2002) Mol Cell Proteomics , vol.1 , pp. 349-356
    • Deane, C.M.1    Salwiski, L.2    Xenarios, I.3    Eisenberg, D.4
  • 27
    • 0037432528 scopus 로고    scopus 로고
    • How reliable are experimental protein-protein interaction data?
    • Sprinzak E, Sattath S, Margalit H, (2003) How reliable are experimental protein-protein interaction data? J Mol Biol 327: 919-923.
    • (2003) J Mol Biol , vol.327 , pp. 919-923
    • Sprinzak, E.1    Sattath, S.2    Margalit, H.3
  • 28
    • 33847744247 scopus 로고    scopus 로고
    • How complete are current yeast and human proteininteraction networks?
    • Hart GT, Ramani A, Marcotte E, (2006) How complete are current yeast and human proteininteraction networks? Genome Biol 7: 120.
    • (2006) Genome Biol , vol.7 , pp. 120
    • Hart, G.T.1    Ramani, A.2    Marcotte, E.3
  • 29
    • 36949000237 scopus 로고    scopus 로고
    • Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps
    • Huang H, Jedynak BM, Bader JS, (2007) Where have all the interactions gone? Estimating the coverage of two-hybrid protein interaction maps. PLoS Comput Biol 3: e214.
    • (2007) PLoS Comput Biol , vol.3
    • Huang, H.1    Jedynak, B.M.2    Bader, J.S.3
  • 33
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein-protein interactions
    • von Mering C, Krause R, Snel B, Cornell M, Oliver SG, et al. (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417: 399-403.
    • (2002) Nature , vol.417 , pp. 399-403
    • von Mering, C.1    Krause, R.2    Snel, B.3    Cornell, M.4    Oliver, S.G.5
  • 34
    • 78650274124 scopus 로고    scopus 로고
    • New insights into protein-protein interaction data lead to increased estimates of the S. cerevisiae interactome size
    • Sambourg L, Thierry-Mieg N, (2010) New insights into protein-protein interaction data lead to increased estimates of the S. cerevisiae interactome size. BMC Bioinformatics 11: 605.
    • (2010) BMC Bioinformatics , vol.11 , pp. 605
    • Sambourg, L.1    Thierry-Mieg, N.2
  • 36
    • 84874396916 scopus 로고    scopus 로고
    • Rapid annotation of anonymous sequences from genome projects using semantic similarities and a weighting scheme in gene ontology
    • Fontana P, Cestaro A, Velasco R, Formentin E, Toppo S, (2009) Rapid annotation of anonymous sequences from genome projects using semantic similarities and a weighting scheme in gene ontology. PLoS One 4: e4619.
    • (2009) PLoS One , vol.4
    • Fontana, P.1    Cestaro, A.2    Velasco, R.3    Formentin, E.4    Toppo, S.5
  • 37
    • 34548655343 scopus 로고    scopus 로고
    • Quantitative sequence-function relationships in proteins based on gene ontology
    • Sangar V, Blankenberg D, Altman N, Lesk A, (2007) Quantitative sequence-function relationships in proteins based on gene ontology. BMC Bioinformatics 8: 294.
    • (2007) BMC Bioinformatics , vol.8 , pp. 294
    • Sangar, V.1    Blankenberg, D.2    Altman, N.3    Lesk, A.4
  • 38
    • 34047202181 scopus 로고    scopus 로고
    • Deciphering protein-protein interactions. Part I. Experimental techniques and databases
    • Shoemaker BA, Panchenko AR, (2007) Deciphering protein-protein interactions. Part I. Experimental techniques and databases. PLoS Comput Biol 3: e42.
    • (2007) PLoS Comput Biol , vol.3
    • Shoemaker, B.A.1    Panchenko, A.R.2
  • 39
    • 0037050004 scopus 로고    scopus 로고
    • Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectometry
    • Ho Y, Gruhler A, Heilbut A, Bader G, Moore L, et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectometry. Nature 415: 180-183.
    • (2002) Nature , vol.415 , pp. 180-183
    • Ho, Y.1    Gruhler, A.2    Heilbut, A.3    Bader, G.4    Moore, L.5
  • 40
    • 0037050026 scopus 로고    scopus 로고
    • Functional organisation of the yeast proteome by systematic analysis of protein complexes
    • Gavin AC, Bosche M, Krause R, Grandi P, (2002) Functional organisation of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141-147.
    • (2002) Nature , vol.415 , pp. 141-147
    • Gavin, A.C.1    Bosche, M.2    Krause, R.3    Grandi, P.4
  • 41
    • 33644555054 scopus 로고    scopus 로고
    • Proteome survey reveals modularity of the yeast cell machinery
    • Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, et al. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440: 631-636.
    • (2006) Nature , vol.440 , pp. 631-636
    • Gavin, A.C.1    Aloy, P.2    Grandi, P.3    Krause, R.4    Boesche, M.5
  • 42
    • 33645453254 scopus 로고    scopus 로고
    • Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
    • Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, et al. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440: 637-643.
    • (2006) Nature , vol.440 , pp. 637-643
    • Krogan, N.J.1    Cagney, G.2    Yu, H.3    Zhong, G.4    Guo, X.5
  • 45
    • 33947364411 scopus 로고    scopus 로고
    • Schizosaccharomyces pombe, comparative genomics: from sequence to systems
    • In: Sunnerhagen P, Piskur J, editors, Topics in Current Genetics
    • Wood V (2006) Schizosaccharomyces pombe, comparative genomics: from sequence to systems. In: Sunnerhagen P, Piskur J, editors. Comparative Genomics. Topics in Current Genetics. pp. 233-285.
    • (2006) Comparative Genomics , pp. 233-285
    • Wood, V.1
  • 47
    • 84890690485 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions on the basis of evolutionary conservation of protein functions
    • Kotelnikova E, Kalinin A, Yuryev A, Maslov S, (2007) Prediction of protein-protein interactions on the basis of evolutionary conservation of protein functions. Evol Bioinform Online 3: 197-206.
    • (2007) Evol Bioinform Online , vol.3 , pp. 197-206
    • Kotelnikova, E.1    Kalinin, A.2    Yuryev, A.3    Maslov, S.4
  • 48
    • 53349117774 scopus 로고    scopus 로고
    • High-quality binary protein interaction map of the yeast interactome network
    • Yu H, Braun P, Yldrm MA, Lemmens I, Venkatesan K, et al. (2008) High-quality binary protein interaction map of the yeast interactome network. Science 322: 104-110.
    • (2008) Science , vol.322 , pp. 104-110
    • Yu, H.1    Braun, P.2    Yldrm, M.A.3    Lemmens, I.4    Venkatesan, K.5
  • 49
    • 84866902745 scopus 로고    scopus 로고
    • The timetree of life
    • Morrison DA, (2009) The timetree of life. Syst Biol 58: 461-462.
    • (2009) Syst Biol , vol.58 , pp. 461-462
    • Morrison, D.A.1
  • 50
    • 61949197412 scopus 로고    scopus 로고
    • High throughput interaction data reveals degree conservation of hub proteins
    • Fox A, Taylor D, Slonim DK, (2009) High throughput interaction data reveals degree conservation of hub proteins. Pac Symp Biocomput pp. 391-402.
    • (2009) Pac Symp Biocomput , pp. 391-402
    • Fox, A.1    Taylor, D.2    Slonim, D.K.3
  • 51
    • 0034943378 scopus 로고    scopus 로고
    • The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes
    • Wagner A, (2001) The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Mol Biol Evol 18: 1283-1292.
    • (2001) Mol Biol Evol , vol.18 , pp. 1283-1292
    • Wagner, A.1
  • 52
    • 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: e25.
    • (2007) PLoS Comput Biol , vol.3
    • Beltrao, P.1    Serrano, L.2
  • 55
    • 0037245913 scopus 로고    scopus 로고
    • BIND: the Biomolecular Interaction Network Database
    • Bader GD, Betel D, Hogue CWV, (2003) BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res 31: 248-250.
    • (2003) Nucleic Acids Res , vol.31 , pp. 248-250
    • Bader, G.D.1    Betel, D.2    Hogue, C.W.V.3
  • 57
    • 58149193234 scopus 로고    scopus 로고
    • STRING 8a global view on proteins and their functional interactions in 630 organisms
    • Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, et al. (2009) STRING 8a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res 37: D412-D416.
    • (2009) Nucleic Acids Res , vol.37
    • Jensen, L.J.1    Kuhn, M.2    Stark, M.3    Chaffron, S.4    Creevey, C.5
  • 61
    • 0142052944 scopus 로고    scopus 로고
    • A bayesian networks approach for predicting protein-protein interactions from genomic data
    • Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, et al. (2003) A bayesian networks approach for predicting protein-protein interactions from genomic data. Science 302: 449-453.
    • (2003) Science , vol.302 , pp. 449-453
    • Jansen, R.1    Yu, H.2    Greenbaum, D.3    Kluger, Y.4    Krogan, N.J.5


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