inria-00133991, version 1
Symbolic Reachability Analysis of Genetic Regulatory Networks using Qualitative Abstractions
(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:
- INRIA – CNRS : UMR5558 – Université Claude Bernard - Lyon I
- 2:
- 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
- http://hal.inria.fr/inria-00133991
- oai:hal.inria.fr:inria-00133991
- From:
- Submitted on: Wednesday, 28 February 2007 12:40:24
- Updated on: Wednesday, 28 February 2007 14:39:30




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