Literature DB >> 18482906

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

D A Rand1.   

Abstract

The dynamical systems arising from gene regulatory, signalling and metabolic networks are strongly nonlinear, have high-dimensional state spaces and depend on large numbers of parameters. Understanding the relation between the structure and the function for such systems is a considerable challenge. We need tools to identify key points of regulation, illuminate such issues as robustness and control and aid in the design of experiments. Here, I tackle this by developing new techniques for sensitivity analysis. In particular, I show how to globally analyse the sensitivity of a complex system by means of two new graphical objects: the sensitivity heat map and the parameter sensitivity spectrum. The approach to sensitivity analysis is global in the sense that it studies the variation in the whole of the model's solution rather than focusing on output variables one at a time, as in classical sensitivity analysis. This viewpoint relies on the discovery of local geometric rigidity for such systems, the mathematical insight that makes a practicable approach to such problems feasible for highly complex systems. In addition, we demonstrate a new summation theorem that substantially generalizes previous results for oscillatory and other dynamical phenomena. This theorem can be interpreted as a mathematical law stating the need for a balance between fragility and robustness in such systems.

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Year:  2008        PMID: 18482906      PMCID: PMC2706458          DOI: 10.1098/rsif.2008.0084.focus

Source DB:  PubMed          Journal:  J R Soc Interface        ISSN: 1742-5662            Impact factor:   4.118


  25 in total

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Journal:  Science       Date:  2002-03-01       Impact factor: 47.728

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Authors:  Marie E Csete; John C Doyle
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3.  Robust oscillations within the interlocked feedback model of Drosophila circadian rhythm.

Authors:  H R Ueda; M Hagiwara; H Kitano
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4.  A detailed predictive model of the mammalian circadian clock.

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5.  Statistical mechanical approaches to models with many poorly known parameters.

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Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2003-08-12

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Journal:  Bioessays       Date:  2002-12       Impact factor: 4.345

7.  Temperature dependency and temperature compensation in a model of yeast glycolytic oscillations.

Authors:  Peter Ruoff; Melinda K Christensen; Jana Wolf; Reinhart Heinrich
Journal:  Biophys Chem       Date:  2003-11-01       Impact factor: 2.352

Review 8.  Limit cycle models for circadian rhythms based on transcriptional regulation in Drosophila and Neurospora.

Authors:  J C Leloup; D Gonze; A Goldbeter
Journal:  J Biol Rhythms       Date:  1999-12       Impact factor: 3.182

9.  The IkappaB-NF-kappaB signaling module: temporal control and selective gene activation.

Authors:  Alexander Hoffmann; Andre Levchenko; Martin L Scott; David Baltimore
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10.  Toward a detailed computational model for the mammalian circadian clock.

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Journal:  Proc Natl Acad Sci U S A       Date:  2003-05-29       Impact factor: 11.205

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  30 in total

1.  Workflow for generating competing hypothesis from models with parameter uncertainty.

Authors:  David Gomez-Cabrero; Albert Compte; Jesper Tegner
Journal:  Interface Focus       Date:  2011-03-30       Impact factor: 3.906

Review 2.  Measurement of single-cell dynamics.

Authors:  David G Spiller; Christopher D Wood; David A Rand; Michael R H White
Journal:  Nature       Date:  2010-06-10       Impact factor: 49.962

3.  Biological switches and clocks.

Authors:  John J Tyson; Reka Albert; Albert Goldbeter; Peter Ruoff; Jill Sible
Journal:  J R Soc Interface       Date:  2008-08-06       Impact factor: 4.118

Review 4.  Sensitivity analysis of infectious disease models: methods, advances and their application.

Authors:  Jianyong Wu; Radhika Dhingra; Manoj Gambhir; Justin V Remais
Journal:  J R Soc Interface       Date:  2013-07-17       Impact factor: 4.118

5.  Sensitivity, robustness, and identifiability in stochastic chemical kinetics models.

Authors:  Michał Komorowski; Maria J Costa; David A Rand; Michael P H Stumpf
Journal:  Proc Natl Acad Sci U S A       Date:  2011-05-06       Impact factor: 11.205

Review 6.  How to deal with parameters for whole-cell modelling.

Authors:  Ann C Babtie; Michael P H Stumpf
Journal:  J R Soc Interface       Date:  2017-08-02       Impact factor: 4.118

Review 7.  Multiscale complexity in the mammalian circadian clock.

Authors:  Yr Yamada; Db Forger
Journal:  Curr Opin Genet Dev       Date:  2010-12       Impact factor: 5.578

8.  Robustness of circadian clocks to daylight fluctuations: hints from the picoeucaryote Ostreococcus tauri.

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Journal:  PLoS Comput Biol       Date:  2010-11-11       Impact factor: 4.475

9.  Robustness from flexibility in the fungal circadian clock.

Authors:  Ozgur E Akman; David A Rand; Paul E Brown; Andrew J Millar
Journal:  BMC Syst Biol       Date:  2010-06-24

10.  Iron behaving badly: inappropriate iron chelation as a major contributor to the aetiology of vascular and other progressive inflammatory and degenerative diseases.

Authors:  Douglas B Kell
Journal:  BMC Med Genomics       Date:  2009-01-08       Impact factor: 3.063

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