Deconstruction and Dynamical Robustness of Regulatory Networks: Application to the Yeast Cell Cycle Networks

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Abstract

Analyzing all the deterministic dynamics of a Boolean regulatory network is a difficult problem since it grows exponentially with the number of nodes. In this paper, we present mathematical and computational tools for analyzing the complete deterministic dynamics of Boolean regulatory networks. For this, the notion of alliance is introduced, which is a subconfiguration of states that remains fixed regardless of the values of the other nodes. Also, equivalent classes are considered, which are sets of updating schedules which have the same dynamics. Using these techniques, we analyze two yeast cell cycle models. Results show the effectiveness of the proposed tools for analyzing update robustness as well as the discovery of new information related to the attractors of the yeast cell cycle models considering all the possible deterministic dynamics, which previously have only been studied considering the parallel updating scheme.

Original languageEnglish
Pages (from-to)939-966
Number of pages28
JournalBulletin of Mathematical Biology
Volume75
Issue number6
DOIs
StatePublished - Jun 2013

Keywords

  • Alliances
  • Attractors
  • Boolean networks
  • Dynamics
  • Update robustness

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