Analysis of the impact degree distribution in metabolic networks using branching process approximation

Physica A: Statistical Mechanics and its Applications

Volumn 391, Issue 1-2, 2012, Pages 379-387

  Takemoto, Kazuhiro ^a,b   Tamura, Takeyuki ^c   Cong, Yang ^d   Ching, Wai Ki ^d   Vert, Jean Philippe ^e,f,g   Akutsu, Tatsuya ^c  

^a JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c KYOTO UNIVERSITY   (Japan)

^d UNIVERSITY OF HONG KONG   (Hong Kong)

^e PSL RESEARCH UNIVERSITY   (France)

^f INSTITUT CURIE   (France)

^g INSERM U900   (France)

Author keywords

Branching process; Cascading failure; Metabolic network; Power law

Indexed keywords

APPROXIMATION THEORY; METABOLISM;

APPROXIMATION METHODS; BRANCHING PROCESS; CASCADING FAILURES; DEGREE DISTRIBUTIONS; METABOLIC NETWORK; POWER-LAW; THEORETICAL FRAMEWORK; THEORY OF BRANCHING PROCESS;

PROBABILITY DISTRIBUTIONS;

EID: 80054041784     PISSN: 03784371     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.physa.2011.08.011     Document Type: Article

References (35)

1. H. Kitano Cancer as a robust system: implications for anticancer therapy Nat. Rev. Cancer 4 2004 227 235 (Pubitemid 38337502)
2. M. Kanehisa, S. Goto, M. Furumichi, M. Tanabe, and M. Hirakawa KEGG for representation and analysis of molecular networks involving diseases and drugs Nucleic Acids Res. 38 2010 D355 D360
3. I.M. Keseler EcoCyc: a comprehensive database of Escherichia coli biology Nucleic Acids Res. 39 2011 D583 D590
4. J.A. Papin, J. Stelling, N.D. Price, S. Klamt, S. Schuster, and B.O. Palsson Comparison of network-based pathway analysis methods Trends Biotechnol. 22 2004 400 405 (Pubitemid 38993223)
5. V. Acua, F. Chierichetti, V. Lacroix, A. Marchetti-Spaccamela, M.F. Sagot, and L. Stougie Modes and cuts in metabolic networks: complexity and algorithms BioSystems 95 2009 51 60
6. A.P. Burgard, P. Pharkya, and C.D. Maranas OptKnock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization Biotechnol. Bioeng. 84 2003 647 657 (Pubitemid 37420336)
7. U.U. Haus, S. Klamt, and T. Stephen Computing knock-out strategies in metabolic networks J. Comput. Biol. 15 2008 259 268 (Pubitemid 351450465)
8. S. Klamt, and E.D. Gilles Minimal cut sets in biochemical reaction networks Bioinformatics 20 2004 226 234 (Pubitemid 38195681)
9. J. Behre, T. Wilhelm, A. von Kamp, E. Ruppin, and S. Schuster Structural robustness of metabolic networks with respect to multiple knockouts J. Theoret. Biol. 252 2008 433 441 (Pubitemid 351681901)
10. D. Deutscher, I. Meilijson, S. Schuster, and E. Ruppin Can single knockouts accurately single out gene functions? BMC Syst. Biol. 2 2008 50
11. T. Handorf, O. Ebenhöh, and R. Heinrich Expanding metabolic networks: scopes of compounds, robustness, and evolution J. Mol. Evol. 61 2005 498 512 (Pubitemid 41416893)
12. N. Lemke, F. Herédia, C.K. Barcellos, A.N. dos Reis, and J.C.M. Mombach Essentiality and damage in metabolic networks Bioinformatics 20 2004 115 119 (Pubitemid 38088348)
13. Z. Li, R.-S. Wang, X.-S. Zhang, and L. Chen Detecting drug targets with minimum side effects in metabolic networks IET Syst. Biol. 3 2009 523 533
14. P. Sridhar, B. Song, T. Kahveci, S. Ranka, Mining metabolic networks for optimal drug targets, in: Proc. Pacific Symposium on Biocomputing 2008, 2008, pp. 291302.
15. T. Tamura, K. Takemoto, and T. Akutsu Finding minimum reaction cuts of metabolic networks under a Boolean model using integer programming and feedback vertex sets Int. J. Knowl. Discov. Bioinform. 1 2009 14 31
16. A.G. Smart, L.A.N. Amaral, and J.M. Ottino Cascading failure and robustness in metabolic networks Proc. Natl. Acad. Sci. USA 105 2008 13223 13228
17. D. Jiang, S. Zhou, and Y.-P.P. Chen Compensatory ability to null mutation in metabolic networks Biotechnol. Bioeng. 103 2009 361 369
18. Y. Cong, T. Tamura, T. Akutsu, W.-K. Ching, Efficient computation of impact degrees for multiple reactions in metabolic networks with cycles, in: Proc. ACM Third International Workshop on Data and Text Mining in Bioinformatics, 2009, pp. 6770.
19. D.-S. Lee, K.-I. Goh, B. Khang, and D. Kim Branching process approach to avalanche dynamics on complex networks J. Korean Phys. Soc. 44 2004 633 637 (Pubitemid 38483475)
20. A. Saichev, A. Helmstetter, and D. Sornette Power-law distributions of offspring and generation numbers in branching models of earthquake triggering Pure Appl. Geophys. 162 2005 1113 1134 (Pubitemid 40782251)
21. T.R. Harris Theory of Branching Processes 1989 Dover New York
22. I. Dobson, B.A. Carreras, and D.E. Newman A loading-dependent model of probabilistic cascading failure Probab. Engrg. Inform. Sci. 19 2005 15 31
23. J. Kim, and I. Dobson Approximating a loading-dependent cascading failure model with a branching process IEEE Trans. Reliab. 59 2010 691 699
24. A. Wagner, and D.A. Fell The small world inside large metabolic networks Proc. R. Soc. Lond. Ser. B 268 2001 1803 1810 (Pubitemid 32844028)
25. S. Light, P. Kraulis, and A. Elofsson Preferential attachment in the evolution of metabolic networks BMC Genomics 6 2005 159
26. C. Pál, B. Papp, and M.J. Lercher Adaptive evolution of bacterial metabolic networks by horizontal gene transfer Nat. Genet. 37 2005 1372 1375 (Pubitemid 41722195)
27. D. Vitkup, P. Kharchenko, and A. Wagner Influence of metabolic network structure and function on enzyme evolution Genome Biol. 7 2006 R39
28. I. Dobson, B.A. Carreras, D.E. Newman, A branching process approximation to cascading load-dependent system failure, in: Proc. 37th Annual Hawaii International Conference on System Sciences, 2004.
29. H. Jeong, B. Tombor, R. Albert, Z.N. Oltvai, and A.-L. Barabási The large-scale organization of metabolic networks Nature 407 2000 651 654
30. R. Albert, and A.-L. Barabási Statistical mechanics of complex networks Rev. Modern Phys. 74 2002 47 97
31. A. Saichev, and D. Sornette Anomalous power law distribution of total lifetimes of branching processes: application to earthquake aftershock sequences Phys. Rev. E 70 2004 046123
32. M.E.J. Newman Power laws, Pareto distributions and Zipf's law Contemp. Phys. 46 2005 323 351 (Pubitemid 41335662)
33. http://www.genome.jp/kegg/pathway.html
34. http://www.genome.jp/kegg/catalog/orglist.html
35. I. Dobson, B.A. Carreras, Number and propagation of line outages in cascading events in electric power transmission systems, in: Proc. 48th Annual Allerton Conference on Communication, Control & Computing, 2010.