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Comparing Discrete and Piecewise Affine Differential Equation Models of Gene Regulatory Networks (Long Version)

Please always quote using this URN:urn:nbn:de:0296-matheon-11672
  • Mathematical modeling often helps to provide a systems perspective on gene regulatory networks. In particular, qualitative approaches are useful when detailed kinetic information is lacking. Multiple methods have been developed that implement qualitative information in different ways, e.g., in purely discrete or hybrid discrete/continuous models. In this paper, we compare the discrete asynchronous logical modeling formalism for gene regulatory networks due to R. Thomas with piecewise affine differential equation models. We provide a local characterization of the qualitative dynamics of a piecewise affine differential equation model using the discrete dynamics of a corresponding Thomas model. Based on this result, we investigate the consistency of higher-level dynamical properties such as attractor characteristics and reachability. We show that although the two approaches are based on equivalent information, the resulting qualitative dynamics are different. In particular, the dynamics of the piecewise affine differential equation model is not a simple refinement of the dynamics of the Thomas model.

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Metadaten
Author:Shahrad Jamshidi, Heike Siebert, Alexander Bockmayr
URN:urn:nbn:de:0296-matheon-11672
Referee:Peter Deuflhard
Document Type:Preprint, Research Center Matheon
Language:English
Date of first Publication:2012/08/15
Release Date:2012/08/15
Tag:Discrete model; Gene regulatory network; Piecewise affine model
Institute:Research Center Matheon
Freie Universität Berlin
MSC-Classification:92-XX BIOLOGY AND OTHER NATURAL SCIENCES / 92Cxx Physiological, cellular and medical topics / 92C42 Systems biology, networks
Preprint Number:980
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