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Volumn 15, Issue 5, 2013, Pages 823-838

Choosing appropriate models for protein-protein interaction networks: A comparison study

Author keywords

Biological mechanism; Performance comparison; PPI network models; Statistical properties

Indexed keywords

PROTEIN; PROTEIN BINDING;

EID: 84887272391     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbt014     Document Type: Article
Times cited : (18)

References (49)
  • 1
    • 0034628508 scopus 로고    scopus 로고
    • A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
    • Uetz P, Giot L, Cagney G, et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000;403:623-27.
    • (2000) Nature , vol.403 , pp. 623-627
    • Uetz, P.1    Giot, L.2    Cagney, G.3
  • 2
    • 0035836765 scopus 로고    scopus 로고
    • A comprehensive two-hybrid analysis to explore the yeast protein interactome
    • Ito T, Chiba T, Ozawa R, et al. A comprehensive two-hybrid analysis to explore the yeast protein interactome. ProcNatl Acad SciUSA 2001;98:4569-74.
    • (2001) ProcNatl Acad SciUSA , vol.98 , pp. 4569-4574
    • Ito, T.1    Chiba, T.2    Ozawa, R.3
  • 3
    • 25144498379 scopus 로고    scopus 로고
    • A human protein-protein interaction network: a resource for annotating the proteome
    • Stelzl U, Worm U, Lalowski M, et al. A human protein-protein interaction network: a resource for annotating the proteome. Cell 2005;122:957-68.
    • (2005) Cell , vol.122 , pp. 957-968
    • Stelzl, U.1    Worm, U.2    Lalowski, M.3
  • 4
    • 0033974688 scopus 로고    scopus 로고
    • Toward a protein-protein interaction map of the budding yeast: a comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins
    • Ito T, Tashiro K, Muta S, et al. Toward a protein-protein interaction map of the budding yeast: a comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. ProcNatl Acad Sci USA 2000;97:1143-7.
    • (2000) ProcNatl Acad Sci USA , vol.97 , pp. 1143-1147
    • Ito, T.1    Tashiro, K.2    Muta, S.3
  • 5
    • 27144530248 scopus 로고    scopus 로고
    • Towards a proteomescale map of the human protein-protein interaction network
    • Rual JF, Venkatesan K, Hao T, et al. Towards a proteomescale map of the human protein-protein interaction network. Nature 2005;437:1173-8.
    • (2005) Nature , vol.437 , pp. 1173-1178
    • Rual, J.F.1    Venkatesan, K.2    Hao, T.3
  • 6
    • 0037050026 scopus 로고    scopus 로고
    • Functional organization of the yeast proteome by systematic analysis of protein complexes
    • Gavin AC, Bösche M, Krause R, et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 2002;415:141-7.
    • (2002) Nature , vol.415 , pp. 141-147
    • Gavin, A.C.1    Bösche, M.2    Krause, R.3
  • 7
    • 33645453254 scopus 로고    scopus 로고
    • Global landscape of protein complexes in the yeast Saccharomyces cerevisiae
    • Krogan NJ, Cagney G, Yu H, et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 2006;440:637-43.
    • (2006) Nature , vol.440 , pp. 637-643
    • Krogan, N.J.1    Cagney, G.2    Yu, H.3
  • 8
    • 0037050004 scopus 로고    scopus 로고
    • Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
    • Ho Y, Gruhler A, Heilbut A, et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 2002;415:180-3.
    • (2002) Nature , vol.415 , pp. 180-183
    • Ho, Y.1    Gruhler, A.2    Heilbut, A.3
  • 9
    • 0035799707 scopus 로고    scopus 로고
    • Lethality and centrality in protein networks
    • Jeong H, Mason SP, Barabási AL, et al. Lethality and centrality in protein networks. Nature 2001;411:41.
    • (2001) Nature , vol.411 , pp. 41
    • Jeong, H.1    Mason, S.P.2    Barabási, A.L.3
  • 10
    • 0032482432 scopus 로고    scopus 로고
    • Collective dynamics of 'smallworld' networks
    • Watts DJ, Strogatz SH. Collective dynamics of 'smallworld' networks. Nature 1998;393:440-2.
    • (1998) Nature , vol.393 , pp. 440-442
    • Watts, D.J.1    Strogatz, S.H.2
  • 11
    • 0035826155 scopus 로고    scopus 로고
    • Exploring complex networks
    • Strogatz SH. Exploring complex networks. Nature 2001; 410:268-76.
    • (2001) Nature , vol.410 , pp. 268-276
    • Strogatz, S.H.1
  • 12
    • 0013173298 scopus 로고    scopus 로고
    • Modeling of protein interaction networks
    • Vazquez A, Flammini A, Maritan A, et al. Modeling of protein interaction networks. Complex Syst 2003;1:38-44.
    • (2003) Complex Syst , vol.1 , pp. 38-44
    • Vazquez, A.1    Flammini, A.2    Maritan, A.3
  • 13
    • 12344273375 scopus 로고    scopus 로고
    • Modeling interactome:scale-free or geometric?
    • Pržulj N, Corneil D.G. Jurisica I. Modeling interactome:scale-free or geometric? Bioinformatics 2004;20:3508-15.
    • (2004) Bioinformatics , vol.20 , pp. 3508-3515
    • Pržulj, N.1    Corneil, D.G.2    Jurisica, I.3
  • 14
    • 33750630691 scopus 로고    scopus 로고
    • Modeling protein-protein interaction networks via a stickiness index
    • Pržulj N, Higham DJ. Modeling protein-protein interaction networks via a stickiness index. J R Soc Interface 2006;3:711-16.
    • (2006) J R Soc Interface , vol.3 , pp. 711-716
    • Pržulj, N.1    Higham, D.J.2
  • 15
    • 85137859893 scopus 로고    scopus 로고
    • Subgraph isomorphism in planar graphs and related problems
    • Eppstein D. Subgraph isomorphism in planar graphs and related problems. JGraph AlgorithmsAppl 1999;3:1-27.
    • (1999) JGraph AlgorithmsAppl , vol.3 , pp. 1-27
    • Eppstein, D.1
  • 16
    • 80052469087 scopus 로고    scopus 로고
    • Network model with structured nodes
    • Frisco P. Network model with structured nodes. PhysRevE StatNonlin SoftMatter Phys 2011;84(2 Pt 1):021931.
    • (2011) PhysRevE StatNonlin SoftMatter Phys , vol.84 , Issue.2 , pp. 021931
    • Frisco, P.1
  • 17
    • 79551578034 scopus 로고    scopus 로고
    • Improving evolutionary models of protein interaction networks
    • Gibson TA, Goldberg DS. Improving evolutionary models of protein interaction networks. Bioinformatics 2011;27:376-82.
    • (2011) Bioinformatics , vol.27 , pp. 376-382
    • Gibson, T.A.1    Goldberg, D.S.2
  • 18
    • 34547558890 scopus 로고    scopus 로고
    • Not all scale-free networks are born equal: the role of the seed graph in PPI network evolution
    • Hormozdiari F, Berenbrink P, Pržulj N, et al. Not all scale-free networks are born equal: the role of the seed graph in PPI network evolution. PLoS Comput Biol 2007; 3:e118.
    • (2007) PLoS Comput Biol , vol.3 , pp. e118
    • Hormozdiari, F.1    Berenbrink, P.2    Pržulj, N.3
  • 20
    • 53349117774 scopus 로고    scopus 로고
    • High-quality binary protein interaction map of the yeast interactome network
    • Yu H, Braun P, Yildirim MA, et al. High-quality binary protein interaction map of the yeast interactome network. Science 2008;322:104-10.
    • (2008) Science , vol.322 , pp. 104-110
    • Yu, H.1    Braun, P.2    Yildirim, M.A.3
  • 21
    • 54949127160 scopus 로고    scopus 로고
    • iRefIndex: a consolidated protein interaction database with provenance
    • Razick S, Magklaras G, Donaldson IM. iRefIndex: a consolidated protein interaction database with provenance. BMC Bioinformatics 2008;9:405.
    • (2008) BMC Bioinformatics , vol.9 , pp. 405
    • Razick, S.1    Magklaras, G.2    Donaldson, I.M.3
  • 22
    • 0347755535 scopus 로고    scopus 로고
    • The Database of Interacting Proteins: 2004 update
    • Salwínski L, Miller CS, Smith AJ, et al. The Database of Interacting Proteins: 2004 update. Nucleic Acids Res 2004; 32:449-51.
    • (2004) Nucleic Acids Res , vol.32 , pp. 449-451
    • Salwínski, L.1    Miller, C.S.2    Smith, A.J.3
  • 23
    • 0041024111 scopus 로고    scopus 로고
    • The TREC-8 question answering track report
    • Gaithersburg, MD, USA: National Institute of Standards and Technology
    • Voorhees EM. The TREC-8 question answering track report. In: Proceedings of the 8th Text Retrieval Conference (TREC8). Gaithersburg, MD, USA: National Institute of Standards and Technology, 1999;77-82.
    • (1999) Proceedings of the 8th Text Retrieval Conference (TREC8) , pp. 77-82
    • Voorhees, E.M.1
  • 25
    • 0038483826 scopus 로고    scopus 로고
    • Emergence of scaling in random networks
    • Barabási AL, Albert R. Emergence of scaling in random networks. Science 1999;286:509-12.
    • (1999) Science , vol.286 , pp. 509-512
    • Barabási, A.L.1    Albert, R.2
  • 26
    • 0036013593 scopus 로고    scopus 로고
    • Statistical mechanics of complex networks
    • Albert R, Barabási AL. Statistical mechanics of complex networks. RevMod Phys 2002;74:47-97.
    • (2002) RevMod Phys , vol.74 , pp. 47-97
    • Albert, R.1    Barabási, A.L.2
  • 27
    • 31044448435 scopus 로고    scopus 로고
    • A simple physical model for scaling in protein-protein interaction networks
    • Deeds EJ, Ashenberg O, Shakhnovich EI. A simple physical model for scaling in protein-protein interaction networks. ProcNatl Acad SciUSA 2006;103:311-16.
    • (2006) ProcNatl Acad SciUSA , vol.103 , pp. 311-316
    • Deeds, E.J.1    Ashenberg, O.2    Shakhnovich, E.I.3
  • 28
    • 61949109355 scopus 로고    scopus 로고
    • Reverse engineering the evolution of protein interaction networks
    • Gibson TA, Goldberg DS. Reverse engineering the evolution of protein interaction networks. Pac Symp Biocomput 2009;190-202.
    • (2009) Pac Symp Biocomput , pp. 190-202
    • Gibson, T.A.1    Goldberg, D.S.2
  • 30
    • 0037460091 scopus 로고    scopus 로고
    • Evolving protein interaction networks through gene duplication
    • Pastor-Satorras R, Smith E, Solé RV. Evolving protein interaction networks through gene duplication. JTheor Biol 2003;222:199-210.
    • (2003) JTheor Biol , vol.222 , pp. 199-210
    • Pastor-Satorras, R.1    Smith, E.2    Solé, R.V.3
  • 31
    • 33750991092 scopus 로고    scopus 로고
    • The degree distribution of the generalized duplication model
    • Bebek G, Berenbrink P, Cooper C, et al. The degree distribution of the generalized duplication model. Theor Comput Sci 2006;369:239-49.
    • (2006) Theor Comput Sci , vol.369 , pp. 239-249
    • Bebek, G.1    Berenbrink, P.2    Cooper, C.3
  • 32
    • 12444301754 scopus 로고    scopus 로고
    • Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplications
    • Berg J, Lässig M, Wagner A. Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplications. BMC Evol Biol 2004; 4:51.
    • (2004) BMC Evol Biol , vol.4 , pp. 51
    • Berg, J.1    Lässig, M.2    Wagner, A.3
  • 33
    • 0346245913 scopus 로고    scopus 로고
    • On the structure of protein-protein interaction networks
    • Thomas A, Cannings R, Monk NA, et al. On the structure of protein-protein interaction networks. Biochem SocTrans 2003;31:1491-6.
    • (2003) Biochem SocTrans , vol.31 , pp. 1491-1496
    • Thomas, A.1    Cannings, R.2    Monk, N.A.3
  • 34
    • 33747837195 scopus 로고    scopus 로고
    • A lock-and-key model for protein-protein interactions
    • Morrison JL, Breitling R, Higham DJ, et al. A lock-and-key model for protein-protein interactions. Bioinformatics 2006; 22:2012-19.
    • (2006) Bioinformatics , vol.22 , pp. 2012-2019
    • Morrison, J.L.1    Breitling, R.2    Higham, D.J.3
  • 35
    • 61949371427 scopus 로고    scopus 로고
    • Learning the structure of protein-protein interaction networks
    • Kuchaiev O, Pržulj N. Learning the structure of protein-protein interaction networks. Pac Symp Biocomput 2009;39-50.
    • (2009) Pac Symp Biocomput , pp. 39-50
    • Kuchaiev, O.1    Pržulj, N.2
  • 38
    • 33846672214 scopus 로고    scopus 로고
    • Biological network comparison using graphlet degree distribution
    • Pržulj N. Biological network comparison using graphlet degree distribution. Bioinformatics 2007;23:e177-83.
    • (2007) Bioinformatics , vol.23 , pp. e177-e183
    • Pržulj, N.1
  • 39
    • 58149213932 scopus 로고    scopus 로고
    • Literature-curated protein interaction datasets
    • Cusick ME, Yu H, Smolyar A, et al. Literature-curated protein interaction datasets. NatMethods 2009;1:39-46.
    • (2009) NatMethods , vol.1 , pp. 39-46
    • Cusick, M.E.1    Yu, H.2    Smolyar, A.3
  • 40
    • 0037245913 scopus 로고    scopus 로고
    • BIND: the Biomolecular Interaction Network Database
    • Bader GD, Betel D, Hogue CWV. BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res 2003;31:248-50.
    • (2003) Nucleic Acids Res , vol.31 , pp. 248-250
    • Bader, G.D.1    Betel, D.2    Hogue, C.W.V.3
  • 41
    • 33644873184 scopus 로고    scopus 로고
    • BioGRID: a general repository for interaction datasets
    • Stark C, Breitkreutz BJ, Reguly T, et al. BioGRID: a general repository for interaction datasets. Nucleic Acids Res 2006;34:535-9.
    • (2006) Nucleic Acids Res , vol.34 , pp. 535-539
    • Stark, C.1    Breitkreutz, B.J.2    Reguly, T.3
  • 43
    • 84859204939 scopus 로고    scopus 로고
    • The IntAct molecular interaction database in 2012
    • Kerrien S, Aranda B, Breuza L, et al. The IntAct molecular interaction database in 2012. Nucleic Acids Res 2012;40:841-6.
    • (2012) Nucleic Acids Res , vol.40 , pp. 841-846
    • Kerrien, S.1    Aranda, B.2    Breuza, L.3
  • 44
    • 75549083295 scopus 로고    scopus 로고
    • MINT, the molecular interaction database: 2009 update
    • Ceol A, Aryamontri AC, Licata L, et al. MINT, the molecular interaction database: 2009 update. Nucleic Acids Res 2010;38:532-9.
    • (2010) Nucleic Acids Res , vol.38 , pp. 532-539
    • Ceol, A.1    Aryamontri, A.C.2    Licata, L.3
  • 46
    • 20144387067 scopus 로고    scopus 로고
    • The MIPS mammalian protein-protein interaction database
    • Pagel P, Kovac S, Oesterheld M, et al. The MIPS mammalian protein-protein interaction database. Bioinformatics 2005;21:832-4.
    • (2005) Bioinformatics , vol.21 , pp. 832-834
    • Pagel, P.1    Kovac, S.2    Oesterheld, M.3
  • 47
    • 18744376914 scopus 로고    scopus 로고
    • Online predicted human interaction database
    • Brown KR, Jurisica I. Online predicted human interaction database. Bioinformatics 2005;21:2076-82.
    • (2005) Bioinformatics , vol.21 , pp. 2076-2082
    • Brown, K.R.1    Jurisica, I.2
  • 48
    • 78651512420 scopus 로고    scopus 로고
    • GraphCrunch 2:software tool for network modeling, alignment and clustering
    • Kuchaiev O, Stevanović A, Hayes W, et al. GraphCrunch 2:software tool for network modeling, alignment and clustering. BMC bioinformatics 2011;12:24.
    • (2011) BMC bioinformatics , vol.12 , pp. 24
    • Kuchaiev, O.1    Stevanović, A.2    Hayes, W.3
  • 49
    • 84924181828 scopus 로고    scopus 로고
    • Towards a theory of scale-free graphs: definition, properties, and implications
    • Li L, Alderson D, Tanaka R, et al. Towards a theory of scale-free graphs: definition, properties, and implications. InternetMath 2005;2:431-523.
    • (2005) InternetMath , vol.2 , pp. 431-523
    • Li, L.1    Alderson, D.2    Tanaka, R.3


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