The dynamics of canalizing Boolean networks

DOI10.1155/2020/3687961MaRDI QIDQ2296155zbMATH OpenOpenAlexWikidataFDO

Authors Elijah Paul, William Qin, Reinhard Laubenbacher, Gleb Pogudin

Publication date 17 February 2020

Published in Complexity (Search for Journal in Brave)

Copyright license Creative Commons Attribution 4.0 International

Full work available at URL https://arxiv.org/abs/1902.00056

Mathematics Subject Classification ID

Systems biology, networks (92C42)

Abstract: Boolean networks are a popular modeling framework in computational biology to capture the dynamics of molecular networks, such as gene regulatory networks. It has been observed that many published models of such networks are defined by regulatory rules driving the dynamics that have certain so-called canalizing properties. In this paper, we investigate the dynamics of a random Boolean network with such properties using analytical methods and simulations. From our simulations, we observe that Boolean networks with higher canalizing depth have generally fewer attractors, the attractors are smaller, and the basins are larger, with implications for the stability and robustness of the models. These properties are relevant to many biological applications. Moreover, our results show that, from the standpoint of the attractor structure, high canalizing depth, compared to relatively small positive canalizing depth, has a very modest impact on dynamics. Motivated by these observations, we conduct mathematical study of the attractor structure of a random Boolean network of canalizing depth one (i.e., the smallest positive depth). For every positive integer $ell$, we give an explicit formula for the limit of the expected number of attractors of length $ell$ in an $n$-state random Boolean network as $n$ goes to infinity.

Review text

Summary: Boolean networks are a popular modeling framework in computational biology to capture the dynamics of molecular networks, such as gene regulatory networks. It has been observed that many published models of such networks are defined by regulatory rules driving the dynamics that have certain so-called canalizing properties. In this paper, we investigate the dynamics of a random Boolean network with such properties using analytical methods and simulations. From our simulations, we observe that Boolean networks with higher canalizing depth have generally fewer attractors, the attractors are smaller, and the basins are larger, with implications for the stability and robustness of the models. These properties are relevant to many biological applications. Moreover, our results show that, from the standpoint of the attractor structure, high canalizing depth, compared to relatively small positive canalizing depth, has a very modest impact on dynamics. Motivated by these observations, we conduct mathematical study of the attractor structure of a random Boolean network of canalizing depth one (i.e., the smallest positive depth). For every positive integer \(\ell \), we give an explicit formula for the limit of the expected number of attractors of length \(\ell\) in an \(n\)-state random Boolean network as \(n\) goes to infinity.

Recommendations

• Boolean nested canalizing functions: a comprehensive analysis
• The influence of canalization on the robustness of Boolean networks
• Nested canalyzing depth and network stability
• Dynamics of complex Boolean networks: canalization, stability, and criticality
• Canalization and symmetry in Boolean models for genetic regulatory networks

Cites work

• An Application of MacMahon’s Master Theorem
• Analytic combinatorics
• Boolean network-based analysis of the apoptosis network: irreversible apoptosis and stable surviving
• Introduction to algorithms.
• Matrices
• Nested canalyzing depth and network stability
• On Ramanujan's Q-function
• On the Lambert \(w\) function
• Preferential Arrangements
• Stratification and enumeration of Boolean functions by canalizing depth
• Superpolynomial growth in the number of attractors in Kauffman networks

Cited in

(12)

• Ordered dynamics in biased and cooperative Boolean networks
• Boolean networks: beyond generalized asynchronicity
• The influence of canalization on the robustness of Boolean networks
• Variable-depth simulation of most permissive Boolean networks
• Stratification and enumeration of Boolean functions by canalizing depth
• Collectively canalizing Boolean functions
• Dynamics of complex Boolean networks: canalization, stability, and criticality
• Canalization and symmetry in Boolean models for genetic regulatory networks
• Bifurcations in Boolean Networks
• Boolean nested canalizing functions: a comprehensive analysis
• Combinatorics of Boolean automata circuits dynamics
• Nested canalyzing depth and network stability

This page was built for publication: The dynamics of canalizing Boolean networks

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q2296155)