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Volumn 8, Issue 10, 2013, Pages

Perturbation Centrality and Turbine: A Novel Centrality Measure Obtained Using a Versatile Network Dynamics Tool

Author keywords

[No Author keywords available]

Indexed keywords

METHIONINE TRANSFER RNA LIGASE;

EID: 84886914488     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0078059     Document Type: Article
Times cited : (27)

References (59)
  • 2
    • 84875170915 scopus 로고    scopus 로고
    • Protein contact networks: an emerging paradigm in chemistry
    • Di Paola L, De Ruvo M, Paci P, Santoni D, Giuliani A, (2013) Protein contact networks: an emerging paradigm in chemistry. Chem Rev 113: 1598-1613.
    • (2013) Chem Rev , vol.113 , pp. 1598-1613
    • Di Paola, L.1    De Ruvo, M.2    Paci, P.3    Santoni, D.4    Giuliani, A.5
  • 3
    • 65649089458 scopus 로고    scopus 로고
    • Intra and inter-molecular communications through protein structure network
    • Vishveshwara S, Ghosh A, Hansia P, (2009) Intra and inter-molecular communications through protein structure network. Curr Protein Pept Sci 10: 146-160.
    • (2009) Curr Protein Pept Sci , vol.10 , pp. 146-160
    • Vishveshwara, S.1    Ghosh, A.2    Hansia, P.3
  • 4
    • 79960149420 scopus 로고    scopus 로고
    • RING: networking interacting residues, evolutionary information and energetics in protein structures
    • Martin AJM, Vidotto M, Boscariol F, Di Domenico T, Walsh I, et al. (2011) RING: networking interacting residues, evolutionary information and energetics in protein structures. Bioinformatics 27: 2003-2005.
    • (2011) Bioinformatics , vol.27 , pp. 2003-2005
    • Martin, A.J.M.1    Vidotto, M.2    Boscariol, F.3    Di Domenico, T.4    Walsh, I.5
  • 6
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: understanding the cell's functional organization
    • Barabási A-L, Oltvai ZN, (2004) Network biology: understanding the cell's functional organization. Nat Rev Genet 5: 101-113.
    • (2004) Nat Rev Genet , vol.5 , pp. 101-113
    • Barabási, A.-L.1    Oltvai, Z.N.2
  • 8
    • 78651324347 scopus 로고    scopus 로고
    • The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored
    • Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, et al. (2011) The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 39: D561-D568.
    • (2011) Nucleic Acids Res , vol.39
    • Szklarczyk, D.1    Franceschini, A.2    Kuhn, M.3    Simonovic, M.4    Roth, A.5
  • 9
    • 0036088133 scopus 로고    scopus 로고
    • DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions
    • Xenarios I, (2002) DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res 30: 303-305.
    • (2002) Nucleic Acids Res , vol.30 , pp. 303-305
    • Xenarios, I.1
  • 11
    • 65649138753 scopus 로고    scopus 로고
    • Perturbation waves in proteins and protein networks: applications of percolation and game theories in signaling and drug design
    • Antal MA, Böde C, Csermely P, (2009) Perturbation waves in proteins and protein networks: applications of percolation and game theories in signaling and drug design. Curr Protein Pept Sci 10: 161-172.
    • (2009) Curr Protein Pept Sci , vol.10 , pp. 161-172
    • Antal, M.A.1    Böde, C.2    Csermely, P.3
  • 12
    • 80555139635 scopus 로고    scopus 로고
    • Implicit methods for qualitative modeling of gene regulatory networks
    • Garg A, Mohanram K, De Micheli G, Xenarios I, (2012) Implicit methods for qualitative modeling of gene regulatory networks. Methods Mol Biol 786: 397-443.
    • (2012) Methods Mol Biol , vol.786 , pp. 397-443
    • Garg, A.1    Mohanram, K.2    De Micheli, G.3    Xenarios, I.4
  • 13
    • 79953109968 scopus 로고    scopus 로고
    • Elementary signaling modes predict the essentiality of signal transduction network components
    • Wang R-S, Albert R, (2011) Elementary signaling modes predict the essentiality of signal transduction network components. BMC Syst Biol 5: 44.
    • (2011) BMC Syst Biol , vol.5 , pp. 44
    • Wang, R.-S.1    Albert, R.2
  • 14
    • 36248971654 scopus 로고    scopus 로고
    • Alternative pathway approach for automating analysis and validation of cell perturbation networks and design of perturbation experiments
    • Gong Y, Zhang Z, (2007) Alternative pathway approach for automating analysis and validation of cell perturbation networks and design of perturbation experiments. Ann N Y Acad Sci 1115: 267-285.
    • (2007) Ann N Y Acad Sci , vol.1115 , pp. 267-285
    • Gong, Y.1    Zhang, Z.2
  • 15
    • 36249005452 scopus 로고    scopus 로고
    • CellFrame: a data structure for abstraction of cell biology experiments and construction of perturbation networks
    • Gong Y, Zhang Z, (2007) CellFrame: a data structure for abstraction of cell biology experiments and construction of perturbation networks. Ann N Y Acad Sci 1115: 249-266.
    • (2007) Ann N Y Acad Sci , vol.1115 , pp. 249-266
    • Gong, Y.1    Zhang, Z.2
  • 16
    • 0036772705 scopus 로고    scopus 로고
    • Gene perturbation and intervention in probabilistic Boolean networks
    • Shmulevich I, Dougherty ER, Zhang W, (2002) Gene perturbation and intervention in probabilistic Boolean networks. Bioinformatics 18: 1319-1331.
    • (2002) Bioinformatics , vol.18 , pp. 1319-1331
    • Shmulevich, I.1    Dougherty, E.R.2    Zhang, W.3
  • 17
    • 69849111694 scopus 로고    scopus 로고
    • ITM Probe: analyzing information flow in protein networks
    • Stojmirovi A, Yu Y-K, Stojmirović A, (2009) ITM Probe: analyzing information flow in protein networks. Bioinformatics 25: 2447-2449.
    • (2009) Bioinformatics , vol.25 , pp. 2447-2449
    • Stojmirovi, A.1    Yu, Y.-K.2    Stojmirović, A.3
  • 18
    • 77950491448 scopus 로고    scopus 로고
    • PerturbationAnalyzer: a tool for investigating the effects of concentration perturbation on protein interaction networks
    • Li F, Li P, Xu W, Peng Y, Bo X, et al. (2010) PerturbationAnalyzer: a tool for investigating the effects of concentration perturbation on protein interaction networks. Bioinformatics 26: 275-277.
    • (2010) Bioinformatics , vol.26 , pp. 275-277
    • Li, F.1    Li, P.2    Xu, W.3    Peng, Y.4    Bo, X.5
  • 19
    • 33747877324 scopus 로고    scopus 로고
    • BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge
    • Calzone L, Fages F, Soliman S, (2006) BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge. Bioinformatics 22: 1805-1807.
    • (2006) Bioinformatics , vol.22 , pp. 1805-1807
    • Calzone, L.1    Fages, F.2    Soliman, S.3
  • 20
    • 84859348190 scopus 로고    scopus 로고
    • Conedy: a scientific tool to investigate complex network dynamics
    • Rothkegel A, Lehnertz K, (2012) Conedy: a scientific tool to investigate complex network dynamics. Chaos 22: 013125.
    • (2012) Chaos , vol.22 , pp. 013125
    • Rothkegel, A.1    Lehnertz, K.2
  • 23
    • 35348813628 scopus 로고    scopus 로고
    • Propagation of large concentration changes in reversible protein-binding networks
    • Maslov S, Ispolatov I, (2007) Propagation of large concentration changes in reversible protein-binding networks. Proc Natl Acad Sci U S A 104: 13655-13660.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 13655-13660
    • Maslov, S.1    Ispolatov, I.2
  • 24
    • 34247960076 scopus 로고
    • The strength of weak ties
    • Granovetter M, (1973) The strength of weak ties. Am J Sociol 78: 1360-1380.
    • (1973) Am J Sociol , vol.78 , pp. 1360-1380
    • Granovetter, M.1
  • 25
    • 77952026080 scopus 로고    scopus 로고
    • Model for rumor spreading over networks
    • Trpevski D, Tang WKS, Kocarev L, (2010) Model for rumor spreading over networks. Phys Rev E 81: 056102.
    • (2010) Phys Rev E , vol.81 , pp. 056102
    • Trpevski, D.1    Tang, W.K.S.2    Kocarev, L.3
  • 26
    • 77549087023 scopus 로고    scopus 로고
    • Percolation and epidemics in random clustered networks
    • Miller JC, (2009) Percolation and epidemics in random clustered networks. Phys Rev E 80: 020901.
    • (2009) Phys Rev E , vol.80 , pp. 020901
    • Miller, J.C.1
  • 27
    • 40949115417 scopus 로고    scopus 로고
    • Impact of community structure on information transfer
    • Danon L, Arenas A, Díaz-Guilera A, (2008) Impact of community structure on information transfer. Phys Rev E 77: 036103.
    • (2008) Phys Rev E , vol.77 , pp. 036103
    • Danon, L.1    Arenas, A.2    Díaz-Guilera, A.3
  • 28
    • 68949111730 scopus 로고    scopus 로고
    • Benchmarks for testing community detection algorithms on directed and weighted graphs with overlapping communities
    • Lancichinetti A, Fortunato S, (2009) Benchmarks for testing community detection algorithms on directed and weighted graphs with overlapping communities. Phys Rev E 80: 016118.
    • (2009) Phys Rev E , vol.80 , pp. 016118
    • Lancichinetti, A.1    Fortunato, S.2
  • 29
    • 77958564958 scopus 로고    scopus 로고
    • Community landscapes: an integrative approach to determine overlapping network module hierarchy, identify key nodes and predict network dynamics
    • Kovács IA, Palotai R, Szalay MS, Csermely P, (2010) Community landscapes: an integrative approach to determine overlapping network module hierarchy, identify key nodes and predict network dynamics. PLoS ONE 5: e12528.
    • (2010) PLoS ONE , vol.5
    • Kovács, I.A.1    Palotai, R.2    Szalay, M.S.3    Csermely, P.4
  • 31
    • 48349116091 scopus 로고    scopus 로고
    • Extremism propagation in social networks with hubs
    • Franks DW, Noble J, Kaufmann P, Stagl S, (2008) Extremism propagation in social networks with hubs. Adapt Behav 16: 264-274.
    • (2008) Adapt Behav , vol.16 , pp. 264-274
    • Franks, D.W.1    Noble, J.2    Kaufmann, P.3    Stagl, S.4
  • 33
    • 14644396645 scopus 로고    scopus 로고
    • Functional cartography of complex metabolic networks
    • Guimerà R, Nunes Amaral LA, (2005) Functional cartography of complex metabolic networks. Nature 433: 895-900.
    • (2005) Nature , vol.433 , pp. 895-900
    • Guimerà, R.1    Nunes Amaral, L.A.2
  • 34
    • 42949165604 scopus 로고    scopus 로고
    • Chaperones as integrators of cellular networks: changes of cellular integrity in stress and diseases
    • Palotai R, Szalay MS, Csermely P, (2008) Chaperones as integrators of cellular networks: changes of cellular integrity in stress and diseases. IUBMB Life 60: 10-18.
    • (2008) IUBMB Life , vol.60 , pp. 10-18
    • Palotai, R.1    Szalay, M.S.2    Csermely, P.3
  • 35
    • 80055081144 scopus 로고    scopus 로고
    • Heat shock partially dissociates the overlapping modules of the yeast protein-protein interaction network: a systems level model of adaptation
    • Mihalik Á, Csermely P, (2011) Heat shock partially dissociates the overlapping modules of the yeast protein-protein interaction network: a systems level model of adaptation. PLoS Comput Biol 7: e1002187.
    • (2011) PLoS Comput Biol , vol.7
    • Mihalik, Á.1    Csermely, P.2
  • 37
    • 0033637153 scopus 로고    scopus 로고
    • Genomic expression programs in the response of yeast cells to environmental changes
    • Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, et al. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241-4257.
    • (2000) Mol Biol Cell , vol.11 , pp. 4241-4257
    • Gasch, A.P.1    Spellman, P.T.2    Kao, C.M.3    Carmel-Harel, O.4    Eisen, M.B.5
  • 38
    • 79959923522 scopus 로고    scopus 로고
    • g:Profiler - a web server for functional interpretation of gene lists (2011 update)
    • Reimand J, Arak T, Vilo J, (2011) g:Profiler - a web server for functional interpretation of gene lists (2011 update). Nucleic Acids Res 39: W307-W315.
    • (2011) Nucleic Acids Res , vol.39
    • Reimand, J.1    Arak, T.2    Vilo, J.3
  • 39
    • 0028878281 scopus 로고
    • Alterations in carbohydrate metabolism during stress: a review of the literature
    • Mizock BA, (1995) Alterations in carbohydrate metabolism during stress: a review of the literature. Am J Med 98: 75-84.
    • (1995) Am J Med , vol.98 , pp. 75-84
    • Mizock, B.A.1
  • 40
    • 0019433557 scopus 로고
    • Regulation of protein synthesis during heat shock
    • Lindquist S, (1981) Regulation of protein synthesis during heat shock. Nature 293: 311-314.
    • (1981) Nature , vol.293 , pp. 311-314
    • Lindquist, S.1
  • 42
    • 0015514970 scopus 로고
    • Will a large complex systembe stable?
    • May R, (1972) Will a large complex systembe stable? Nature 238: 413-414.
    • (1972) Nature , vol.238 , pp. 413-414
    • May, R.1
  • 43
    • 35648944297 scopus 로고    scopus 로고
    • A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis
    • Ghosh A, Vishveshwara S, (2007) A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis. Proc Natl Acad Sci U S A 104: 15711-15716.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 15711-15716
    • Ghosh, A.1    Vishveshwara, S.2
  • 44
    • 77957231785 scopus 로고    scopus 로고
    • Induced fit, conformational selection and independent dynamic segments: an extended view of binding events
    • Csermely P, Palotai R, Nussinov R, (2010) Induced fit, conformational selection and independent dynamic segments: an extended view of binding events. Trends Biochem Sci 35: 539-546.
    • (2010) Trends Biochem Sci , vol.35 , pp. 539-546
    • Csermely, P.1    Palotai, R.2    Nussinov, R.3
  • 46
    • 34248332629 scopus 로고    scopus 로고
    • Functional residues serve a dominant role in mediating the cooperativity of the protein ensemble
    • Liu T, Whitten ST, Hilser VJ, (2007) Functional residues serve a dominant role in mediating the cooperativity of the protein ensemble. Proc Natl Acad Sci U S A 104: 4347-4352.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 4347-4352
    • Liu, T.1    Whitten, S.T.2    Hilser, V.J.3
  • 47
    • 46449101584 scopus 로고    scopus 로고
    • Discrete breathers in protein structures
    • Piazza F, Sanejouand Y-H, (2008) Discrete breathers in protein structures. Phys Biol 5: 026001.
    • (2008) Phys Biol , vol.5 , pp. 026001
    • Piazza, F.1    Sanejouand, Y.-H.2
  • 48
    • 33847377573 scopus 로고    scopus 로고
    • A robustness-based approach to systems-oriented drug design
    • Kitano H, (2007) A robustness-based approach to systems-oriented drug design. Nat Rev Drug Discov 6: 202-210.
    • (2007) Nat Rev Drug Discov , vol.6 , pp. 202-210
    • Kitano, H.1
  • 49
    • 81355154050 scopus 로고    scopus 로고
    • Dynamical and structural analysis of a T cell survival network identifies novel candidate therapeutic targets for large granular lymphocyte leukemia
    • Saadatpour A, Wang R-S, Liao A, Liu X, Loughran TP, et al. (2011) Dynamical and structural analysis of a T cell survival network identifies novel candidate therapeutic targets for large granular lymphocyte leukemia. PLoS Comput Biol 7: e1002267.
    • (2011) PLoS Comput Biol , vol.7
    • Saadatpour, A.1    Wang, R.-S.2    Liao, A.3    Liu, X.4    Loughran, T.P.5
  • 50
    • 15044349115 scopus 로고    scopus 로고
    • The efficiency of multi-target drugs: the network approach might help drug design
    • Csermely P, Ágoston V, Pongor S, (2005) The efficiency of multi-target drugs: the network approach might help drug design. Trends Pharmacol Sci 26: 178-182.
    • (2005) Trends Pharmacol Sci , vol.26 , pp. 178-182
    • Csermely, P.1    Ágoston, V.2    Pongor, S.3
  • 51
    • 81755184126 scopus 로고    scopus 로고
    • Allo-network drugs: harnessing allostery in cellular networks
    • Nussinov R, Tsai C-J, Csermely P, (2011) Allo-network drugs: harnessing allostery in cellular networks. Trends Pharmacol Sci 32: 686-693.
    • (2011) Trends Pharmacol Sci , vol.32 , pp. 686-693
    • Nussinov, R.1    Tsai, C.-J.2    Csermely, P.3
  • 52
    • 84877580262 scopus 로고    scopus 로고
    • Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review
    • Csermely P, Korcsmáros T, Kiss HJM, London G, Nussinov R, (2013) Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review. Pharmacol Ther 138: 333-408.
    • (2013) Pharmacol Ther , vol.138 , pp. 333-408
    • Csermely, P.1    Korcsmáros, T.2    Kiss, H.J.M.3    London, G.4    Nussinov, R.5
  • 53
    • 36048944020 scopus 로고    scopus 로고
    • Kinetic insulation as an effective mechanism for achieving pathway specificity in intracellular signaling networks
    • Behar M, Dohlman HG, Elston TC, (2007) Kinetic insulation as an effective mechanism for achieving pathway specificity in intracellular signaling networks. Proc Natl Acad Sci U S A 104: 16146-16151.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 16146-16151
    • Behar, M.1    Dohlman, H.G.2    Elston, T.C.3
  • 54
    • 0003509593 scopus 로고    scopus 로고
    • 3rd ed. Sedra AS, Lightner MR, New York: Oxford University Press
    • Chen C-T (1998) Linear System Theory and Design. 3rd ed. Sedra AS, Lightner MR, New York: Oxford University Press.
    • (1998) Linear System Theory and Design
    • Chen, C.-T.1
  • 55
  • 56
    • 3042553224 scopus 로고    scopus 로고
    • Structure of mammalian cytochrome P450 2B4 complexed with 4-(4-chlorophenyl)imidazole at 1.9-A resolution: insight into the range of P450 conformations and the coordination of redox partner binding
    • Scott EE, White MA, He YA, Johnson EF, Stout CD, et al. (2004) Structure of mammalian cytochrome P450 2B4 complexed with 4-(4-chlorophenyl)imidazole at 1.9-A resolution: insight into the range of P450 conformations and the coordination of redox partner binding. J Biol Chem 279: 27294-27301.
    • (2004) J Biol Chem , vol.279 , pp. 27294-27301
    • Scott, E.E.1    White, M.A.2    He, Y.A.3    Johnson, E.F.4    Stout, C.D.5
  • 59
    • 43349094507 scopus 로고    scopus 로고
    • The igraph software package for complex network research
    • Csardi G, Nepusz T (2006) The igraph software package for complex network research. InterJournal Complex Systems: 1695.
    • (2006) InterJournal Complex Systems , pp. 1695
    • Csardi, G.1    Nepusz, T.2


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