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

stabilityBoolean networksgene networkscanalyzation

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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• Nested canalyzing, unate cascade, and polynomial functions

Cited in

(20)

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

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