Modeling and Analysis of Gene Regulatory Networks - Modeling in Computational Biology and Biomedicine - page 44

Chapter 2
Modeling and Analysis of Gene Regulatory
Networks

Gilles Bernot, Jean-Paul Comet, Adrien Richard, Madalena Chaves,
Jean-Luc Gouze, and Frederic 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
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M. Chaves · J.-L. Gouze
Inria Sophia Antipolis Mediterranee, Biocore project-team, 2004 Route des Lucioles, 06902
Sophia Antipolis, France
e-mail: [e-mail] ; [e-mail]
F. D a y a n
SOBIOS SA, 2229 Route des Cretes, 06560 Valbonne Sophia Antipolis, France
e-mail: [e-mail]