Uncovering operational interactions in genetic networks using asynchronous boolean dynamics

Laurent Tournier 1, * Madalena Chaves 1
* Auteur correspondant
1 COMORE - Modeling and control of renewable resources
LOV - Laboratoire d'océanographie de Villefranche, CRISAM - Inria Sophia Antipolis - Méditerranée
Abstract : To analyze and gain intuition on the mechanisms of complex systems of large dimensions, one strategy is to simplify the model by identifying a reduced system, in the form of a smaller set of variables and interactions that still capture specific properties of the system. For large models of biological networks, the diagram of interactions is often well represented by a Boolean model with a family of logical rules. The state space of a Boolean model is finite, and its asynchronous dynamics are fully described by a transition graph in the state space. In this context, a method will be developed for identifying the active or operational interactions responsible for a given dynamic behaviour. The first step in this procedure is the decomposition of the asynchronous transition graph into its strongly connected components, to obtain a ``reduced'' and hierarchically organized graph of transitions. The second step consists of the identification of a partial graph of interactions and a sub-family of logical rules that remain operational in a given region of the state space. This model reduction method and its usefulness are illustrated by an application to a model of programmed cell death. The method identifies two mechanisms used by the cell to respond to death-receptor stimulation and decide between the survival or apoptotic pathways.
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Rapport
[Research Report] RR-6703, INRIA. 2008
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Laurent Tournier, Madalena Chaves. Uncovering operational interactions in genetic networks using asynchronous boolean dynamics. [Research Report] RR-6703, INRIA. 2008. 〈inria-00325914v2〉

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