Quantification of degeneracy in biological systems for characterization of functional interactions between modules

Journal of Theoretical Biology

Volumn 302, Issue , 2012, Pages 29-38

  Li, Yao ^a   Dwivedi, Gaurav ^b   Huang, Wen ^c   Kemp, Melissa L ^b   Yi, Yingfei ^a,d  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

^b Emory University   (United States)

^c UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

^d JILIN UNIVERSITY   (China)

Author keywords

Biological networks; Complexity; Degeneracy; Robustness; Systems biology

Indexed keywords

BIOCHEMICAL COMPOSITION; BIOLOGICAL ANALYSIS; FUNCTIONAL MORPHOLOGY; HOMEOSTASIS; QUANTITATIVE ANALYSIS; REACTION KINETICS;

ARTICLE; BIOLOGICAL NETWORK; COMPLEXITY; DEGENERACY; DYNAMICAL SYSTEM; EVOLUTION; EVOLUTIONARY PRESSURE; HOMEOSTASIS; MATHEMATICAL COMPUTING; PREDATOR PREY INTERACTION; PRIORITY JOURNAL; ROBUSTNESS; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

ALGORITHMS; ANIMALS; BIOLOGICAL EVOLUTION; HOMEOSTASIS; MODELS, BIOLOGICAL; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

EID: 84862784276     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2012.02.020     Document Type: Article

References (34)

1. Becker V., Schilling M., Bachmann J., Baumann U., Raue A., Maiwald T., Timmer J., Klingmüller U. Covering a broad dynamic range: information processing at the erythropoietin receptor. Science 2010, 328(5984):1404.
2. Bogachev V., Krylov N., Röckner M. Elliptic and parabolic equations for measures. Russ. Math. Surv. 2009, 64:973.
3. Chen, W.W., Schoeberl, B., Jasper, P.J., Niepel, M., Nielsen, U.B., Lauffenburger, D.A., Sorger, P.K., 2009. Input-output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data. Mol. Syst. Biol. 5 (1).
4. Constantinescu S., Ghaffari S., Lodish H. The erythropoietin receptor: structure, activation and intracellular signal transduction. Trends Endocrinol. Metab. 1999, 10(1):18-23.
5. Day M. Regularity of boundary quasi-potentials for planar systems. Appl. Math. Optim. 1994, 30(1):79-101.
6. Day M., Darden T. Some regularity results on the Ventcel-Freidlin quasi-potential function. Appl. Math. Optim. 1985, 13(1):259-282.
7. Doyle J., Csete M. Rules of engagement. Nature 2007, 446(7138):860.
8. Edelman G., Gally J. Degeneracy and complexity in biological systems. Proc. Natl. Acad. Sci. 2001, 98(24):13763.
9. Freǐ dlin M., Wentzell A. Random Perturbations of Dynamical Systems 1998, vol. 260. Springer Verlag.
10. Hartwell L., Hopfield J., Leibler S., Murray A., et al. From molecular to modular cell biology. Nature 1999, 402(6761):47.
11. Hennessy B., Smith D., Ram P., Lu Y., Mills G. Exploiting the PI3K/AKT pathway for cancer drug discovery. Nat. Rev. Drug Discovery 2005, 4(12):988-1004.
12. Huang, W., Liu, Z., Ji, M., Yi, Y., 2011. Stochastic stability of invariant measures: part I. Fokker-Planck equations, preprint.
13. Kelly-Welch A., Hanson E., Boothby M., Keegan A. Interleukin-4 and interleukin-13 signaling connections maps. Science 2003, 300(5625):1527.
14. Kitano, H., 2007. Towards a theory of biological robustness. Mol. Syst. Biol. 3 (1).
15. Lander A. Pattern, growth, and control. Cell 2011, 144(6):955-969.
16. Li, Y., Yi, Y. Random perturbation in the vicinity of attractor, preprint.
17. Lu X., Malumbres R., Shields B., Jiang X., Sarosiek K., Natkunam Y., Tiganis T., Lossos I. PTP1B is a negative regulator of interleukin 4-induced STAT6 signaling. Blood 2008, 112(10):4098.
18. Ludwig D. Persistence of dynamical systems under random perturbations. SIAM Rev. 1975, 605-640.
19. Myers M., Andersen J., Cheng A., Tremblay M., Horvath C., Parisien J., Salmeen A., Barford D., Tonks N. TYK2 and JAK2 are substrates of protein-tyrosine phosphatase 1b. J. Biol. Chem. 2001, 276(51):47771.
20. Oda, K., Matsuoka, Y., Funahashi, A., Kitano, H., 2005. A comprehensive pathway map of epidermal growth factor receptor signaling. Mol. Syst. Biol. 1 (1).
21. Pesin Y. Dimension Theory in Dynamical Systems: Contemporary Views and Applications 1997, University of Chicago Press.
22. Rizk A., Batt G., Fages F., Soliman S. A general computational method for robustness analysis with applications to synthetic gene networks. Bioinformatics 2009, 25(12):i169.
23. Röchman Y., Spolski R., Leonard W. New insights into the regulation of T cells by γc family cytokines. Nat. Rev. Immunol. 2009, 9(7):480-490.
24. Sharma P., Chakraborty R., Wang L., Min B., Tremblay M., Kawahara T., Lambeth J., Haque S. Redox regulation of interleukin-4 signaling. Immunity 2008, 29(4):551-564.
25. Shuai K., Liu B. Regulation of JAK-STAT signalling in the immune system. Nat. Rev. Immunol. 2003, 3(11):900-911.
26. Stelling J., Sauer U., Szallasi Z., Doyle F., Doyle J. Robustness of cellular functions. Cell 2004, 118(6):675-685.
27. Sun Han T. Multiple mutual informations and multiple interactions in frequency data. Inf. Control 1980, 46(1):26-45.
28. Swameye I., Müller T., Timmer J., Sandra O., Klingmüller U. Identification of nucleocytoplasmic cycling as a remote sensor in cellular signaling by databased modeling. Proc. Natl. Acad. Sci. USA 2003, 100(3):1028.
29. Tononi G., Sporns O., Edelman G. A measure for brain complexity: relating functional segregation and integration in the nervous system. Proc. Natl. Acad. Sci. 1994, 91(11):5033.
30. Tononi G., Sporns O., Edelman G. Measures of degeneracy and redundancy in biological networks. Proc. Natl. Acad. Sci. USA 1999, 96(6):3257.
31. van Wageningen S., Kemmeren P., Lijnzaad P., Margaritis T., Benschop J., de Castro I., van Leenen D., Groot Koerkamp M., Ko C., Miles A., et al. Functional overlap and regulatory links shape genetic interactions between signaling pathways. Cell 2010, 143(6):991-1004.
32. Wang D., Moriggl R., Stravopodis D., Carpino N., Marine J., Teglund S., Feng J., Ihle J. A small amphipathic α-helical region is required for transcriptional activities and proteasome-dependent turnover of the tyrosine-phosphorylated STAT5. EMBO J. 2000, 19(3):392-399.
33. Xiao D., Li W. Limit cycles for the competitive three dimensional Lotka-Volterra system. J. Differential Equations 2000, 164(1):1-15.
34. Yeung R. A First Course in Information Theory 2002, vol. 1. Plenum Pub Corp.