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Volumn 8, Issue 1, 2014, Pages

Protein interaction networks as metric spaces: A novel perspective on distribution of hubs

Author keywords

Core periphery structure; Essential proteins; Hubs; Metric spaces; Power law graphs; Protein interaction networks; Topological centrality

Indexed keywords

ARABIDOPSIS THALIANA; ESCHERICHIA COLI; SACCHAROMYCES CEREVISIAE;

EID: 84892473115     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-8-6     Document Type: Article
Times cited : (38)

References (38)
  • 1
    • 74549134502 scopus 로고    scopus 로고
    • Human cancer protein-protein interaction network: a structural perspective
    • 10.1371/journal.pcbi.1000601, 2785480, 20011507
    • Kar G, Gursoy A, Keskin O. Human cancer protein-protein interaction network: a structural perspective. PLoS Comput Biol 2009, 5(12):e1000601. 10.1371/journal.pcbi.1000601, 2785480, 20011507.
    • (2009) PLoS Comput Biol , vol.5 , Issue.12
    • Kar, G.1    Gursoy, A.2    Keskin, O.3
  • 2
    • 34547672876 scopus 로고    scopus 로고
    • Assessing significance of connectivity and conservation in protein interaction networks
    • 10.1089/cmb.2007.R014, 17691892
    • Koyutürk M, Szpankowski W, Grama A. Assessing significance of connectivity and conservation in protein interaction networks. J Comput Biol 2007, 14(6):747-764. 10.1089/cmb.2007.R014, 17691892.
    • (2007) J Comput Biol , vol.14 , Issue.6 , pp. 747-764
    • Koyutürk, M.1    Szpankowski, W.2    Grama, A.3
  • 3
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: understanding the cell's functional organization
    • 10.1038/nrg1272, 14735121
    • Barabasi AL, Oltvai ZN. Network biology: understanding the cell's functional organization. Nat Rev Genet 2004, 5(2):101-113. [http://www.ncbi.nlm.nih.gov/pubmed/14735121], 10.1038/nrg1272, 14735121.
    • (2004) Nat Rev Genet , vol.5 , Issue.2 , pp. 101-113
    • Barabasi, A.L.1    Oltvai, Z.N.2
  • 4
    • 33745712594 scopus 로고    scopus 로고
    • Why do hubs tend to be essential in protein networks?
    • 10.1371/journal.pgen.0020088, 1473040, 16751849
    • He X, Zhang J. Why do hubs tend to be essential in protein networks?. PLoS Genet 2006, 2(6):e88. 10.1371/journal.pgen.0020088, 1473040, 16751849.
    • (2006) PLoS Genet , vol.2 , Issue.6
    • He, X.1    Zhang, J.2
  • 6
    • 65449152586 scopus 로고    scopus 로고
    • Identifying hubs in protein interaction networks
    • 10.1371/journal.pone.0005344, 2670494, 19399170
    • Vallabhajosyula R, Chakravarti D, Lutfeali S, Ray A, Raval A. Identifying hubs in protein interaction networks. PLoS One 2009, 4(4):e5344. 10.1371/journal.pone.0005344, 2670494, 19399170.
    • (2009) PLoS One , vol.4 , Issue.4
    • Vallabhajosyula, R.1    Chakravarti, D.2    Lutfeali, S.3    Ray, A.4    Raval, A.5
  • 7
    • 33746631391 scopus 로고    scopus 로고
    • Evolutionary and physiological importance of hub proteins
    • 10.1371/journal.pcbi.0020088, 1500817, 16839197
    • Batada N, Hurst L, Tyers M. Evolutionary and physiological importance of hub proteins. PLoS Comput Biol 2006, 2(7):e88. 10.1371/journal.pcbi.0020088, 1500817, 16839197.
    • (2006) PLoS Comput Biol , vol.2 , Issue.7
    • Batada, N.1    Hurst, L.2    Tyers, M.3
  • 8
    • 16344381521 scopus 로고    scopus 로고
    • Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks
    • 10.1093/molbev/msi072, 15616139
    • Hahn MW, Kern AD. Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Mol Biol Evol 2005, 22(4):803-806. [http://www.ncbi.nlm.nih.gov/pubmed/15616139], 10.1093/molbev/msi072, 15616139.
    • (2005) Mol Biol Evol , vol.22 , Issue.4 , pp. 803-806
    • Hahn, M.W.1    Kern, A.D.2
  • 9
    • 2442477788 scopus 로고    scopus 로고
    • Genomic analysis of essentiality within protein networks
    • 10.1016/j.tig.2004.04.008, 15145574
    • Yu H, Greenbaum D, Xin Lu H, Zhu X, Gerstein M. Genomic analysis of essentiality within protein networks. Trends Genet 2004, 20(6):227-231. [http://www.ncbi.nlm.nih.gov/pubmed/15145574], 10.1016/j.tig.2004.04.008, 15145574.
    • (2004) Trends Genet , vol.20 , Issue.6 , pp. 227-231
    • Yu, H.1    Greenbaum, D.2    Xin Lu, H.3    Zhu, X.4    Gerstein, M.5
  • 10
    • 34247622363 scopus 로고    scopus 로고
    • The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics
    • Yu H, Kim PM, Sprecher E, Trifonov V, Gerstein M. The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol 2007, 3(4):8. [http://www.ncbi.nlm.nih.gov/pubmed/17447836].
    • (2007) PLoS Comput Biol , vol.3 , Issue.4 , pp. 8
    • Yu, H.1    Kim, P.M.2    Sprecher, E.3    Trifonov, V.4    Gerstein, M.5
  • 11
    • 84865968015 scopus 로고    scopus 로고
    • Detection of protein complexes using a protein ranking algorithm
    • 10.1002/prot.24130, 22685080
    • Zaki N, Berengueres J, Efimov D. Detection of protein complexes using a protein ranking algorithm. Proteins 2012, 80(10):2459-2468. [http://www.ncbi.nlm.nih.gov/pubmed/22685080], 10.1002/prot.24130, 22685080.
    • (2012) Proteins , vol.80 , Issue.10 , pp. 2459-2468
    • Zaki, N.1    Berengueres, J.2    Efimov, D.3
  • 12
    • 84877859040 scopus 로고    scopus 로고
    • Protein complex detection using interaction reliability assessment and weighted clustering coefficient
    • 10.1186/1471-2105-14-163, 3680028, 23688127
    • Zaki N, Efimov D, Berengueres J. Protein complex detection using interaction reliability assessment and weighted clustering coefficient. BMC Bioinformatics 2013, 14:163. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3680028&tool=pmcentrez&rendertype=abstract], 10.1186/1471-2105-14-163, 3680028, 23688127.
    • (2013) BMC Bioinformatics , vol.14 , pp. 163
    • Zaki, N.1    Efimov, D.2    Berengueres, J.3
  • 13
    • 57649232146 scopus 로고    scopus 로고
    • A structural approach for finding functional modules from large biological networks
    • Mete M, Tang F, Xu X, Yuruk N. A structural approach for finding functional modules from large biological networks. BMC Bioinformatics 2008, 9(Suppl 9):S19. [http://www.ncbi.nlm.nih.gov/pubmed/18793464].
    • (2008) BMC Bioinformatics , vol.9 , Issue.SUPPL. 9
    • Mete, M.1    Tang, F.2    Xu, X.3    Yuruk, N.4
  • 14
    • 0033245711 scopus 로고    scopus 로고
    • The centrality of groups and classes
    • Everett M, Borgatti S. The centrality of groups and classes. J Math Sociol 1999, 23(3):181-201.
    • (1999) J Math Sociol , vol.23 , Issue.3 , pp. 181-201
    • Everett, M.1    Borgatti, S.2
  • 15
    • 22944452969 scopus 로고    scopus 로고
    • A measure of betweenness centrality based on random walks
    • [Comment: 15 pages, 7 figures, 2 tables]
    • Newman MEJ. A measure of betweenness centrality based on random walks. 2003, [http://arxiv.org/abs/cond-mat/0309045] [Comment: 15 pages, 7 figures, 2 tables].
    • (2003)
    • Newman, M.E.J.1
  • 16
    • 33845955474 scopus 로고    scopus 로고
    • Inferring topology from clustering coefficients in protein-protein interaction networks
    • 10.1186/1471-2105-7-519, 1716184, 17137490
    • Friedel CC, Zimmer R. Inferring topology from clustering coefficients in protein-protein interaction networks. BMC Bioinformatics 2006, 7:519. [http://www.ncbi.nlm.nih.gov/pubmed/17137490], 10.1186/1471-2105-7-519, 1716184, 17137490.
    • (2006) BMC Bioinformatics , vol.7 , pp. 519
    • Friedel, C.C.1    Zimmer, R.2
  • 17
    • 47949110360 scopus 로고    scopus 로고
    • Centrality, network capacity, and modularity as parameters to analyze the core-periphery structure in metabolic networks
    • Silva M, Ma HMH, Zeng APZAP. Centrality, network capacity, and modularity as parameters to analyze the core-periphery structure in metabolic networks. Proc IEEE 2008, 96(8):1411-1420.
    • (2008) Proc IEEE , vol.96 , Issue.8 , pp. 1411-1420
    • Silva, M.1    Ma, H.M.H.2
  • 19
    • 0034676455 scopus 로고    scopus 로고
    • Surfing the p53 network
    • 10.1038/35042675, 11099028
    • Vogelstein B, Lane D, Levine AJ. Surfing the p53 network. Nature 2000, 408(6810):307-310. 10.1038/35042675, 11099028.
    • (2000) Nature , vol.408 , Issue.6810 , pp. 307-310
    • Vogelstein, B.1    Lane, D.2    Levine, A.J.3
  • 20
    • 0012624911 scopus 로고    scopus 로고
    • Prediction of protein essentiality based on genomic data
    • Jeong H, Barab AL, Oltvai ZN. Prediction of protein essentiality based on genomic data. Complexus 2003, 1:19-28.
    • (2003) Complexus , vol.1 , pp. 19-28
    • Jeong, H.1    Barab, A.L.2    Oltvai, Z.N.3
  • 21
    • 65249094269 scopus 로고    scopus 로고
    • Essential core of protein-protein interaction network in Escherichia coli
    • 10.1021/pr8008786, 19231892
    • Lin CC, Juan HF, Hsiang JT, Hwang YC, Mori H, Huang HC. Essential core of protein-protein interaction network in Escherichia coli. J Proteome Res 2009, 8(4):1925-1931. 10.1021/pr8008786, 19231892.
    • (2009) J Proteome Res , vol.8 , Issue.4 , pp. 1925-1931
    • Lin, C.C.1    Juan, H.F.2    Hsiang, J.T.3    Hwang, Y.C.4    Mori, H.5    Huang, H.C.6
  • 22
    • 84891446988 scopus 로고    scopus 로고
    • Dynamics of the cell-cycle network under genome-rewiring perturbations
    • 10.1088/1478-3975/10/6/066001, 24162518
    • Katzir Y, Elhanati Y, Averbukh I, Braun E. Dynamics of the cell-cycle network under genome-rewiring perturbations. Phys Biol 2013, 10(6):066001. [http://iopscience.iop.org/1478-3975/10/6/066001/article/], 10.1088/1478-3975/10/6/066001, 24162518.
    • (2013) Phys Biol , vol.10 , Issue.6 , pp. 066001
    • Katzir, Y.1    Elhanati, Y.2    Averbukh, I.3    Braun, E.4
  • 23
    • 77956364250 scopus 로고    scopus 로고
    • Topological Centrality and its e-Science Applications
    • Zhuge H, Zhang J. Topological Centrality and its e-Science Applications. J Am Soc Inf Sci Technol 2010, 61(9):1824-1841.
    • (2010) J Am Soc Inf Sci Technol , vol.61 , Issue.9 , pp. 1824-1841
    • Zhuge, H.1    Zhang, J.2
  • 24
    • 78650209059 scopus 로고    scopus 로고
    • Features analysis for identification of date and party hubs in protein interaction network of Saccharomyces Cerevisiae
    • 10.1186/1752-0509-4-172, 3018396, 21167069
    • Mirzarezaee M, Araabi BN, Sadeghi M. Features analysis for identification of date and party hubs in protein interaction network of Saccharomyces Cerevisiae. BMC Syst Biol 2010, 4:172. 10.1186/1752-0509-4-172, 3018396, 21167069.
    • (2010) BMC Syst Biol , vol.4 , pp. 172
    • Mirzarezaee, M.1    Araabi, B.N.2    Sadeghi, M.3
  • 25
    • 77951898121 scopus 로고    scopus 로고
    • Hub promiscuity in protein-protein interaction networks
    • 10.3390/ijms11041930, 2871146, 20480050
    • Patil A, Kinoshita K, Nakamura H. Hub promiscuity in protein-protein interaction networks. Int J Mol Sci 2010, 11(4):1930-1943. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2871146&tool=pmcentrez&rendertype=abstract], 10.3390/ijms11041930, 2871146, 20480050.
    • (2010) Int J Mol Sci , vol.11 , Issue.4 , pp. 1930-1943
    • Patil, A.1    Kinoshita, K.2    Nakamura, H.3
  • 26
    • 33745855141 scopus 로고    scopus 로고
    • Graph theoretic modeling of large-scale semantic networks
    • 10.1016/j.jbi.2005.10.007, 16442849
    • Bales ME, Johnson SB. Graph theoretic modeling of large-scale semantic networks. J Biomed Inform 2006, 39(4):451-464. [http://www.ncbi.nlm.nih.gov/pubmed/16442849], 10.1016/j.jbi.2005.10.007, 16442849.
    • (2006) J Biomed Inform , vol.39 , Issue.4 , pp. 451-464
    • Bales, M.E.1    Johnson, S.B.2
  • 27
    • 0036013593 scopus 로고    scopus 로고
    • Statistical mechanics of complex networks
    • Albert R, Barabasi AL. Statistical mechanics of complex networks. Rev Modern Phys 2002, 74:47. [http://www.springer.com/physics/theoretical,+mathematical+&+computational+physics/book/978-3-540-40372-2].
    • (2002) Rev Modern Phys , vol.74 , pp. 47
    • Albert, R.1    Barabasi, A.L.2
  • 28
    • 0032482432 scopus 로고    scopus 로고
    • Collective dynamics of 'small-world' networks
    • 10.1038/30918, 9623998
    • Watts DJ, Strogatz SH. Collective dynamics of 'small-world' networks. Nature 1998, 393(6684):440-442. [http://www.ncbi.nlm.nih.gov/pubmed/9623998], 10.1038/30918, 9623998.
    • (1998) Nature , vol.393 , Issue.6684 , pp. 440-442
    • Watts, D.J.1    Strogatz, S.H.2
  • 30
    • 0003535772 scopus 로고
    • Boston: Allyn and Bacon
    • Dugundji J. Topology 1974, Boston: Allyn and Bacon.
    • (1974) Topology
    • Dugundji, J.1
  • 32
    • 0642285840 scopus 로고    scopus 로고
    • Preferential attachment in the protein network evolution
    • Eisenberg E, Levanon EY. Preferential attachment in the protein network evolution. Phys Rev Lett 2003, 91(13):138701. [http://arxiv.org/abs/cond-mat/0303490].
    • (2003) Phys Rev Lett , vol.91 , Issue.13 , pp. 138701
    • Eisenberg, E.1    Levanon, E.Y.2
  • 33
    • 79551578034 scopus 로고    scopus 로고
    • Improving evolutionary models of protein interaction networks
    • 10.1093/bioinformatics/btq623, 3031028, 21067999
    • Gibson TA, Goldberg DS. Improving evolutionary models of protein interaction networks. Bioinformatics 2011, 27(3):376-382. [http://www.ncbi.nlm.nih.gov/pubmed/21067999], 10.1093/bioinformatics/btq623, 3031028, 21067999.
    • (2011) Bioinformatics , vol.27 , Issue.3 , pp. 376-382
    • Gibson, T.A.1    Goldberg, D.S.2
  • 34
    • 0035627527 scopus 로고    scopus 로고
    • A random graph model for power law graphs
    • Aiello W, Chung F, Lu L. A random graph model for power law graphs. Exp Math 2001, 10:53-66. [http://www.emis.ams.org/journals/EM/restricted/10/10.1/aiello.ps].
    • (2001) Exp Math , vol.10 , pp. 53-66
    • Aiello, W.1    Chung, F.2    Lu, L.3
  • 35
    • 65449131622 scopus 로고    scopus 로고
    • Core and periphery structures in protein interaction networks
    • Luo F, Li B, Wan XF, Scheuermann RH. Core and periphery structures in protein interaction networks. BMC Bioinformatics 2009, 10(Suppl 4):S8. [http://www.ncbi.nlm.nih.gov/pubmed/19426456].
    • (2009) BMC Bioinformatics , vol.10 , Issue.SUPPL. 4
    • Luo, F.1    Li, B.2    Wan, X.F.3    Scheuermann, R.H.4
  • 36
    • 77952310528 scopus 로고    scopus 로고
    • A human functional protein interaction network and its application to cancer data analysis
    • 10.1186/gb-2010-11-5-r53, 2898064, 20482850
    • Wu G, Feng X, Stein L. A human functional protein interaction network and its application to cancer data analysis. Genome Biol 2010, 11(5):R53. 10.1186/gb-2010-11-5-r53, 2898064, 20482850.
    • (2010) Genome Biol , vol.11 , Issue.5
    • Wu, G.1    Feng, X.2    Stein, L.3
  • 37
    • 75449092046 scopus 로고    scopus 로고
    • AtPIN: Arabidopsis thaliana protein interaction network
    • 10.1186/1471-2105-10-454, 2810305, 20043823
    • Brandão MM, Dantas LL, Silva-Filho MC. AtPIN: Arabidopsis thaliana protein interaction network. BMC Bioinformatics 2009, 10:454. [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2810305&tool=pmcentrez&rendertype=abstract], 10.1186/1471-2105-10-454, 2810305, 20043823.
    • (2009) BMC Bioinformatics , vol.10 , pp. 454
    • Brandão, M.M.1    Dantas, L.L.2    Silva-Filho, M.C.3
  • 38
    • 2942534526 scopus 로고    scopus 로고
    • R-MAT: A recursive model for graph mining
    • Chakrabarti D, Zhan Y, Faloutsos C. R-MAT: A recursive model for graph mining. Computer 2004, 6:442-446. [http://repository.cmu.edu/cgi/viewcontent.cgi?article=1541&context=compsci].
    • (2004) Computer , vol.6 , pp. 442-446
    • Chakrabarti, D.1    Zhan, Y.2    Faloutsos, C.3


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