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inria-00133991, version 1

Symbolic Reachability Analysis of Genetic Regulatory Networks using Qualitative Abstractions

Grégory Batt () a1, Delphine Ropers () b1, Hidde De Jong () b1, Michel Page () c1, Johannes Geiselmann () d2

(2007)

Abstract: The switch-like character of gene regulation has motivated the use of hybrid, discrete-continuous models of genetic regulatory networks. While powerful techniques for the analysis, verification, and control of hybrid systems have been developed, the specificities of the biological application domain pose a number of challenges, notably the absence of quantitative information on parameter values and the size and complexity of networks of biological interest. We introduce a method for the analysis of reachability properties of genetic regulatory networks that is based on a class of discontinuous piecewise-affine (PA) differential equations well-adapted to the above constraints. More specifically, we introduce a hyperrectangular partition of the state space that forms the basis for a discrete abstraction preserving the sign of the derivatives of the state variables. The resulting discrete transition system provides a conservative approximation of the qualitative dynamics of the network and can be efficiently computed in a symbolic manner from inequality constraints on the parameters. The method has been implemented in the computer tool Genetic Network Analyzer (GNA), which has been applied to the analysis of a regulatory system whose functioning is not well-understood by biologists, the nutritional stress response in the bacterium Escherichia coli.

  • a –  Center for Information and Systems Engineering and Center for BioDynamics, Boston University
  • b –  INRIA
  • c –  Université Pierre Mendès-France - Grenoble II, Ecole Supérieure des Affaires
  • d –  Université Joseph Fourier - Grenoble I
  • 1:  HELIX (INRIA Rhône-Alpes)
  • INRIA – CNRS : UMR5558 – Université Claude Bernard - Lyon I
  • 2:  Laboratoire Adaptation et pathogénie des micro-organismes (LAPM)
  • CNRS : UMR5163 – Université Joseph Fourier - Grenoble I
  • Domain : Computer Science/Bioinformatics
    Computer Science/Modeling and Simulation
  • Keywords : piecewise-affine differential equations – qualitative analysis – discrete abstraction – hybrid systems – genetic regulatory networks – systems biology – nutritional stress response – Escherichia coli
  • Available versions :  v1 (2007-02-28) v2 (2007-03-01)
 
  • inria-00133991, version 1
  • oai:hal.inria.fr:inria-00133991
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  • Submitted on: Wednesday, 28 February 2007 12:40:24
  • Updated on: Wednesday, 28 February 2007 14:39:30