Mapping global sensitivity of cellular network dynamics: Sensitivity heat maps and a global summation law

Journal of the Royal Society Interface

Volumn 5, Issue SUPPL. 1, 2008, Pages

  Rand, D A ^a  

^a UNIVERSITY OF WARWICK   (United Kingdom)

Author keywords

Circadian clocks; Mathematical models; Regulatory networks; Robustness; Sensitivity; Signalling networks

Indexed keywords

CELLULAR NEURAL NETWORKS; CELLULAR TELEPHONE SYSTEMS; CONTROL THEORY; DESIGN OF EXPERIMENTS; DYNAMICAL SYSTEMS; FUNCTION EVALUATION; LARGE SCALE SYSTEMS; LAWS AND LEGISLATION; MAPS; MILITARY DATA PROCESSING; MODAL ANALYSIS; ROBUST CONTROL; SCHRODINGER EQUATION; STATE SPACE METHODS;

BALANCE (WEIGHTING); CELLULAR NETWORKS; COMPLEX SYSTEMS; DYNAMICAL PHENOMENA; GRAPHICAL OBJECTS; HIGH-DIMENSIONAL; METABOLIC NETWORKS; NEW TECHNIQUES; OUTPUT VARIABLES; PARAMETER SENSITIVITIES; STATE SPACES; STRONGLY NONLINEAR;

SENSITIVITY ANALYSIS;

IMMUNOGLOBULIN ENHANCER BINDING PROTEIN;

ARTICLE; DYNAMICS; FEASIBILITY STUDY; GEOMETRY; HEAT; MATHEMATICAL MODEL; OSCILLATION; SENSITIVITY ANALYSIS; SIGNAL TRANSDUCTION;

EID: 46249083801     PISSN: 17425689     EISSN: 17425662     Source Type: Journal    
DOI: 10.1098/rsif.2008.0084.focus     Document Type: Article

References (30)

1. Brown, K. S. & Sethna, J. P. 2003 Statistical mechanical approaches to models with many poorly known parameters. Phys. Rev. E 68(Pt 1), 021904. (doi:10.1103/PhysRevE.68.021904)
2. Brown, K. S., Hill, C. C., Calero, G. A., Myers, C. R., Lee, K. H., Sethna, J. P. & Cerione, R. A. 2004 The statistical mechanics of complex signaling networks: nerve growth factor signaling. Phys. Biol. 1, 184-195. (doi:10.1088/1478-3967/1/3/006)
3. Campolongo, F., Saltelli, A., Sorensen, T. & Tarantola, S. 2000 Hitchhiker's guide to sensitivity analysis. In Sensitivity analysis (eds A. Saltelli, K. Chan & E. M. Scott). Wiley series in probability and statistics, pp. 15-47. New York, NY: Wiley.
4. Cox, L. G. E. 2005 A comparison study of sensitivity analyses on two different models concerning the NFκB regulatory module. Technische Universiteit Eindhoven report 05/BMT/S01.
5. Csete, M. E. & Doyle, J. C. 2002 Reverse engineering of biological complexity. Science 295, 1664-1669. (doi:10.1126/science.1069981)
6. Fell, D. A. 1997 Understanding the control of metabolism. London, UK: Portland Press.
7. Forger, D. B. & Peskin, C. S. 2003 A detailed predictive model of the mammalian circadian clock. Proc. Natl Acad. Sci. USA 100, 14 806-14 811. (doi:10.1073/pnas.2036281100)
8. Gutenkunst, R. N., Waterfall, J. J., Casey, F. P., Brown, K. S., Myers, C. R. & Sethna, J. P. 2007 Universally sloppy parameter sensitivities in systems biology models. PLoS Comput. Biol. 3, e189. (doi:10.1371/journal.pcbi.0030189)
9. Heinrich, R. & Schuster, S. 1996 The regulation of cellular systems. New York, NY: Chapman and Hall.
10. Hoffmann, A., Levchenko, A., Scott, M. L. & Baltimore, D. 2002 The IκB-NF-κB signaling module: temporal control and selective gene activation. Science 298, 1241-1245. (doi:10.1126/science.1071914)
11. Hwang, J. T., Dougherty, E. P., Rabitz, S. & Rabitz, H. 1978 The Green's function method of sensitivity analysis in chemical kinetics. J. Chem. Phys. 69, 5180-5191. (doi:10.1063/1.436465)
12. Ihekwaba, A. E. C., Broomhead, D. S., Grimley, R., Benson, N. & Kell, D. B. 2004 Sensitivity analysis of parameters controlling oscillatory signalling in the NF-κB pathway: the roles of IKK and IκBα. IEE Syst. Biol. 1, 93-103. (doi:10.1049/sb:20045009)
13. Kacser, H., Burns, J. A. & Fell, D. A. 1995 The control of flux. Biochem. Soc. Trans. 23, 341-366.
14. Kitano, H. 2002 Systems biology: a brief overview. Science 295, 1662-1664. (doi:10.1126/science.1069492)
15. Kitano, H. 2004 Opinon: cancer as a robust system: implications for anticancer therapy. Nat. Rev. Cancer 4, 227-235. (doi:10.1038/nrc1300)
16. Kitano, H. 2007 Towards a theory of biological robustness. Mol. Syst. Biol. 3, 137. (doi:10.1038/msb4100179)
17. Leloup, J. C. & Goldbeter, A. 2003 Toward a detailed computational model for the mammalian circadian clock. Proc. Natl Acad. Sci. USA 100, 7051-7056. (doi:10.1073/pnas.1132112100)
18. Leloup, J. C., Gonze, D. & Goldbeter, A. 1999 Limit cycle models for circadian rhythms based on transcriptional regulation in Drosophila and Neurospora. J. Biol. Rhythm 14, 433-448. (doi:10.1177/ 074873099129000948)
19. Nelson, D. E. et al. 2004 Oscillations in NF-κB signaling control the dynamics of gene expression. Science 306, 704-708. (doi:10.1126/science.1099962)
20. Rand, D. A., Shulgin, B. V., Salazar, D. & Millar, A. J. 2004 Design principles underlying circadian clocks. J. R. Soc. Interface 1, 119-130. (doi:10.1098/rsif.2004.0014)
21. Rand, D. A., Shulgin, B. V., Salazar, J. D. & Millar, A. J. 2006 Uncovering the design principles of circadian clocks: mathematical analysis of flexibility and evolutionary goals. J. Theor. Biol. 238, 616-635. (doi:10.1016/j.jtbi.2005.06.026)
22. Ruoff, P., Christensen, M. K., Wolf, J. & Heinrich, R. 2003 Temperature dependency and temperature compensation in a model of yeast glycolytic oscillations. Biophys. Chem. 106, 179-192. (doi:10.1016/S0301-4622(03)00191-1)
23. Stelling, J., Gilles, E. D. & Doyle, F. J. 2004a Robustness properties of circadian clock architectures. Proc. Natl Acad. Sci. USA 101, 13 210-13 215. (doi:10.1073/pnas.0401463101)
24. Stelling, J., Sauer, U., Szallasi, Z., Doyle, F. J. & Doyle, J. 2004b Robustness of cellular functions. Cell 118, 675-685. (doi:10.1016/j.cell.2004.09.008)
25. Tiana, G., Krishna, S., Pigolotti, S., Jensen, M. H. & Sneppen, K. 2007 Oscillations and temporal signalling in cells. Phys. Biol. 4, R1-R17. (doi:10.1088/1478-3975/4/2/R01)
26. Tyson, J. J., Hong, C. I., Thron, C. D. & Novak, B. 1999 A simple model of circadian rhythms based on dimerization and proteolysis of PER and TIM. Biophys. J. 77, 2411-2417.
27. Tyson, J. J., Csikasz-Nagy, A. & Novak, B. 2002 The dynamics of cell cycle regulation. Bioessays 24, 1095-1109. (doi:10.1002/bies. 10191)
28. Ueda, H. R., Hagiwara, M. & Kitano, H. 2001 Robust oscillations within the interlocked feedback model of Drosophila circadian rhythm. J. Theor. Biol. 210, 401-406. (doi:10.1006/jtbi.2000.2226)
29. Waterfall, J. J., Casey, F. P., Gutenkunst, R. N., Brown, K. S., Myers, C. R., Brouwer, P. W., Elser, V. & Sethna, J. P. 2006 Sloppy-model universality class and the Vandermonde matrix. Phys. Rev. Lett. 97, 150601. (doi:10.1103/Phys-RevLett.97.150601)
30. Yue, H., Brown, M., Knowles, J., Wang, H., Broomhead, D. S. & Kell, D. B. 2006 Insights into the behaviour of systems biology models from dynamic sensitivity and identifiability analysis: a case study of a NF-κB signalling pathway. Mol. BioSyst. 2, 640-649. (doi:10.1039/ b609442b)