Skip to Main content Skip to Navigation
Reports

Symbolic Reachability Analysis of Genetic Regulatory Networks using Qualitative Abstractions

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.
Complete list of metadatas

Cited literature [51 references]  Display  Hide  Download

https://hal.inria.fr/inria-00133991
Contributor : Rapport de Recherche Inria <>
Submitted on : Thursday, March 1, 2007 - 3:59:00 PM
Last modification on : Monday, February 10, 2020 - 4:36:45 PM
Document(s) archivé(s) le : Tuesday, September 21, 2010 - 12:56:10 PM

Files

RR-6136.pdf
Files produced by the author(s)

Identifiers

Collections

Citation

Grégory Batt, Delphine Ropers, Hidde de Jong, Michel Page, Johannes Geiselmann. Symbolic Reachability Analysis of Genetic Regulatory Networks using Qualitative Abstractions. [Research Report] RR-6136, INRIA. 2007. ⟨inria-00133991v2⟩

Share

Metrics

Record views

294

Files downloads

272