An efficient method for dynamic analysis of gene regulatory networks and in silico gene perturbation experiments

Authors:
Abhishek Garg;Ioannis Xenarios;Luis Mendoza;Giovanni DeMicheli
Affiliations:
Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland;Merck Serono, Geneva, Switzerland;Instituto de Investigaciones Biomédicas, UNAM, Mexico;Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
Venue:
RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology
Year:
2007

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Abstract

With the increasing availability of experimental data on gene-gene and protein-protein interactions, modeling of gene regulatory networks has gained a special attention lately. To have a better understanding of these networks it is necessary to capture their dynamical properties, by computing its steady states. Various methods have been proposed to compute steady states but almost all of them suffer from the state space explosion problem with the increasing size of the networks. Hence it becomes difficult to model even moderate sized networks using these techniques. In this paper, we present a new representation of gene regulatory networks, which facilitates the steady state computation of networks as large as 1200 nodes and 5000 edges. We benchmarked and validated our algorithm on the T helper model from [8] and performed in silico knock out experiments: showing both a reduction in computation time and correct steady state identification.