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Dynamical and topological robustness of the mammalian cell cycle network: A reverse engineering approach

Ruz, Gonzalo A.; Goles, Eric; Montalva, Marco; Fogel, Gary B.

Authors

Gonzalo A. Ruz

Eric Goles

Marco Montalva

Gary B. Fogel



Abstract

A common gene regulatory network model is the threshold Boolean network, used for example to model the Arabidopsis thaliana floral morphogenesis network or the fission yeast cell cycle network. In this paper, we analyze a logical model of the mammalian cell cycle network and its threshold Boolean network equivalent. Firstly, the robustness of the network was explored with respect to update perturbations, in particular, what happened to the attractors for all the deterministic updating schemes. Results on the number of different limit cycles, limit cycle lengths, basin of attraction size, for all the deterministic updating schemes were obtained through mathematical and computational tools. Secondly, we analyzed the topology robustness of the network, by reconstructing synthetic networks that contained exactly the same attractors as the original model by means of a swarm intelligence approach. Our results indicate that networks may not be very robust given the great variety of limit cycles that a network can obtain depending on the updating scheme. In addition, we identified an omnipresent network with interactions that match with the original model as well as the discovery of new interactions. The techniques presented in this paper are general, and can be used to analyze other logical or threshold Boolean network models of gene regulatory networks. © 2013 Elsevier Ireland Ltd.

Citation

Ruz, G. A., Goles, E., Montalva, M., & Fogel, G. B. (2014). Dynamical and topological robustness of the mammalian cell cycle network: A reverse engineering approach. BioSystems, 115(1), 23-32. https://doi.org/10.1016/j.biosystems.2013.10.007

Journal Article Type Article
Acceptance Date Oct 30, 2013
Online Publication Date Nov 6, 2013
Publication Date Jan 1, 2014
Deposit Date Mar 5, 2020
Journal BioSystems
Print ISSN 0303-2647
Electronic ISSN 1872-8324
Publisher Elsevier
Peer Reviewed Peer Reviewed
Volume 115
Issue 1
Pages 23-32
DOI https://doi.org/10.1016/j.biosystems.2013.10.007
Keywords General Biochemistry, Genetics and Molecular Biology; Modelling and Simulation; Statistics and Probability; Applied Mathematics; General Medicine
Public URL https://uwe-repository.worktribe.com/output/5608342
Additional Information This article is maintained by: Elsevier; Article Title: Dynamical and topological robustness of the mammalian cell cycle network: A reverse engineering approach; Journal Title: Biosystems; CrossRef DOI link to publisher maintained version: https://doi.org/10.1016/j.biosystems.2013.10.007; Content Type: article; Copyright: Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.