Multistate nested canalizing functions and their networks

DOI10.1016/J.TCS.2017.01.031MaRDI QIDQ528485zbMATH OpenOpenAlexFDO

Authors C. Kadelka, Yuan Li, Jack Kuipers, J. O. Adeyeye, Reinhard Laubenbacher

Publication date 12 May 2017

Published in Theoretical Computer Science (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1411.4067

zbMATH Keywords

canalizationDerrida plotdiscrete dynamical systemnested canalizing functionrobustnessstability

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Systems biology, networks (92C42)

Abstract: This paper provides a collection of mathematical and computational tools for the study of robustness in nonlinear gene regulatory networks, represented by time- and state-discrete dynamical systems taking on multiple states. The focus is on networks governed by nested canalizing functions (NCFs), first introduced in the Boolean context by S. Kauffman. After giving a general definition of NCFs we analyze the class of such functions. We derive a formula for the normalized average $c$-sensitivities of multistate NCFs, which enables the calculation of the Derrida plot, a popular measure of network stability. We also provide a unique canonical parametrized polynomial form of NCFs. This form has several consequences. We can easily generate NCFs for varying parameter choices, and derive a closed form formula for the number of such functions in a given number of variables, as well as an asymptotic formula. Finally, we compute the number of equivalence classes of NCFs under permutation of variables. Together, the results of the paper represent a useful mathematical framework for the study of NCFs and their dynamic networks.

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Cites work

• Algebraic Models and Their Use in Systems Biology
• Boolean nested canalizing functions: a comprehensive analysis
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• Exploring complex networks
• scientific article; zbMATH DE number 729555 (Why is no real title available?)
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• Maximal sensitivity of Boolean nested canalizing functions
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• Regulatory patterns in molecular interaction networks
• Stratification and enumeration of Boolean functions by canalizing depth
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• The number and probability of canalizing functions
• The number of multistate nested canalyzing functions

Cited in

(15)

• A characterization of nested canalyzing functions with maximum average sensitivity
• The influence of canalization on the robustness of Boolean networks
• Revealing the canalizing structure of Boolean functions: algorithms and applications
• Maximal sensitivity of Boolean nested canalizing functions
• Stratification and enumeration of Boolean functions by canalizing depth
• Nested canalyzing, unate cascade, and polynomial functions
• Quantifying the total effect of edge interventions in discrete multistate networks
• Collectively canalizing Boolean functions
• Boolean nested canalizing functions: a comprehensive analysis
• Nested canalyzing depth and network stability
• The number of multistate nested canalyzing functions
• Certificate complexity and symmetry of nested canalizing functions
• From multivalued to Boolean functions: preservation of soft nested canalization
• Average sensitivity of nested canalizing multivalued functions
• Verification, enumeration and generation of multistate canalizing functions

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