Chapter 2 Modeling and Analysis of Gene Regulatory Networks Gilles Bernot, Jean-Paul Comet, Adrien Richard, Madalena Chaves, Jean-Luc Gouz´ e, and Fr´ ed´ eric Dayan 2.1 Introduction In many ways, a living cell can be compared to a complex factory animated by molecular nanomachines, mainly proteins complexes. Hence it is easy to conceive that the expression of proteins, which are cellular effectors, cannot be constant. On the contrary, it is highly dependent on the general context; environmental conditions (pH, temperature, oxygenation, nutrient availability), developmental stage of an organism (fetal spectrum of proteins differ from adult proteins in mammals), response to a stress (UV irradiation, presence of a chemical toxic, osmotic pressure alteration) and even diseases (cancer, attack of a pathogen) are examples of contextual changes in the level of protein expression. In order to understand this cellular state plasticity, a simplified view of this machinery, following general transfers of information according to the central dogma of molecular biology, is the sequence of events: (1) stimulation via a signaling pathway (e.g. presence of an environmental stimulation, followed by internal transduction of the signal), (2) effective stimulation of a transcription factor, (3) activation of the transcription of a particular gene, (4) production of messenger RNA (mRNA) (see Fig. 2.1), (5) translation of mRNA, i.e. production of a functional G. Bernot () · J.-P. Comet · A. Richard I3S – UMR 6070 CNRS/UNSA, Algorithmes-Euclide-B, 2000 Route des Lucioles, B.P. 121, 06903 Sophia Antipolis, France e-mail: bernot@unice.fr; comet@unice.fr; richard@unice.fr M. Chaves · J.-L. Gouz´ e Inria Sophia Antipolis M´ editerran´ ee, Biocore project-team, 2004 Route des Lucioles, 06902 Sophia Antipolis, France e-mail: madalena.chaves@inria.fr; jean-luc.gouze@inria.fr F. Dayan SOBIOS SA, 2229 Route des Crˆ etes, 06560 Valbonne Sophia Antipolis, France e-mail: frederic.dayan@sobios.com F. Cazals and P. Kornprobst (eds.), Modeling in Computational Biology and Biomedicine, DOI 10.1007/978-3-642-31208-3 2, © Springer-Verlag Berlin Heidelberg 2013 47