Nested canalyzing depth and network stability

DOI10.1007/S11538-011-9692-YMaRDI QIDQ417364zbMATH OpenOpenAlexWikidataFDO

Authors Lori Layne, M. Macauley, Elena S. Dimitrova

Publication date 14 May 2012

Published in Bulletin of Mathematical Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1111.2759

zbMATH Keywords

Boolean networkscanalyzationgene networksstability

Mathematics Subject Classification ID

Systems biology, networks (92C42)

Abstract: We introduce the nested canalyzing depth of a function, which measures the extent to which it retains a nested canalyzing structure. We characterize the structure of functions with a given depth and compute the expected activities and sensitivities of the variables. This analysis quantifies how canalyzation leads to higher stability in Boolean networks. It generalizes the notion of nested canalyzing functions (NCFs), which are precisely the functions with maximum depth. NCFs have been proposed as gene regulatory network models, but their structure is frequently too restrictive and they are extremely sparse. We find that functions become decreasingly sensitive to input perturbations as the canalyzing depth increases, but exhibit rapidly diminishing returns in stability. Additionally, we show that as depth increases, the dynamics of networks using these functions quickly approach the critical regime, suggesting that real networks exhibit some degree of canalyzing depth, and that NCFs are not significantly better than functions of sufficient depth for many applications of the modeling and reverse engineering of biological networks.

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Cites work

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Cited in

(21)

• A characterization of nested canalyzing functions with maximum average sensitivity
• The influence of canalization on the robustness of Boolean networks
• Regulatory patterns in molecular interaction networks
• Revealing the canalizing structure of Boolean functions: algorithms and applications
• Maximal sensitivity of Boolean nested canalizing functions
• The dynamics of canalizing Boolean networks
• Stratification and enumeration of Boolean functions by canalizing depth
• Nested canalyzing, unate cascade, and polynomial functions
• Entropy analysis of Boolean network reduction according to the determinative power of nodes
• Collectively canalizing Boolean functions
• Inferring biologically relevant models: nested canalyzing functions
• Boolean nested canalizing functions: a comprehensive analysis
• Nestedness in networks: A theoretical model and some applications
• Certificate complexity and symmetry of nested canalizing functions
• Interplay between degree and Boolean rules in the stability of Boolean networks
• Logical reduction of biological networks to their most determinative components
• Multistate nested canalizing functions and their networks
• Discrete Models of Biochemical Networks: The Toric Variety of Nested Canalyzing Functions
• Activity in Boolean networks
• Average sensitivity of nested canalizing multivalued functions
• Modular control of Boolean network models

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