Regulatory patterns in molecular interaction networks

DOI10.1016/J.JTBI.2011.08.015zbMATH Open1397.92257arXiv1102.3739OpenAlexW2004114069WikidataQ44968759 ScholiaQ44968759MaRDI QIDQ1786444FDOQ1786444

Authors: David Murrugarra, Reinhard Laubenbacher 

Publication date: 24 September 2018

Published in: Journal of Theoretical Biology (Search for Journal in Brave)

Abstract: Understanding design principles of molecular interaction networks is an important goal of molecular systems biology. Some insights have been gained into features of their network topology through the discovery of graph theoretic patterns that constrain network dynamics. This paper contributes to the identification of patterns in the mechanisms that govern network dynamics. The control of nodes in gene regulatory, signaling, and metabolic networks is governed by a variety of biochemical mechanisms, with inputs from other network nodes that act additively or synergistically. This paper focuses on a certain type of logical rule that appears frequently as a regulatory pattern. Within the context of the multistate discrete model paradigm, a rule type is introduced that reduces to the concept of nested canalyzing function in the Boolean network case. It is shown that networks that employ this type of multivalued logic exhibit more robust dynamics than random networks, with few attractors and short limit cycles. It is also shown that the majority of regulatory functions in many published models of gene regulatory and signaling networks are nested canalyzing.

Full work available at URL: https://arxiv.org/abs/1102.3739

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zbMATH Keywords

robustnessmathematical modelsignalinggene regulationnested canalyzing function

Mathematics Subject Classification ID

Applications of graph theory (05C90) Biochemistry, molecular biology (92C40) Systems biology, networks (92C42)

Cites Work

• Petri net modelling of biological regulatory networks
• Nested canalyzing, unate cascade, and polynomial functions
• From structure to dynamics: frequency tuning in the p53-Mdm2 network. I: Logical approach
• Dynamical behaviour of biological regulatory networks. II: Immunity control in bacteriophage lambda

Cited In (31)

• Structure-function relations are subtle in genetic regulatory networks
• To signal a conjunction of many inputs negative regulation is likely
• Maximal switchability of centralized networks
• The maximal coordination principle in regulatory Boolean networks
• Analyzing steady states of dynamics of bio-molecules from the structure of regulatory networks
• Quantifying the total effect of edge interventions in discrete multistate networks
• Structure of regulatory networks and diversity of gene expression patterns
• Proteomic waves in networks of transcriptional regulators
• Regulatory dynamics on random networks: asymptotic periodicity and modularity
• The influence of canalization on the robustness of Boolean networks
• Genetic and logic networks with the signal-inhibitor-activator structure are dynamically robust
• Dominant vertices in regulatory networks dynamics
• Multistate nested canalizing functions and their networks
• ``Immunetworks, intersecting circuits and dynamics
• Property Preservation along Embedding of Biological Regulatory Networks
• Extending combinatorial regulatory network modeling to include activity control and decay modulation
• Stability and structural properties of gene regulation networks with coregulation rules
• From multivalued to Boolean functions: preservation of soft nested canalization
• Average sensitivity of nested canalizing multivalued functions
• Dynamic modularity in discrete-time models of regulatory networks
• Identification of biological regulatory networks from process hitting models
• Embedding of biological regulatory networks and property preservation
• Regulatory Signals in Genomic Sequences
• The number of multistate nested canalyzing functions
• Methods for and results from the study of design principles in molecular systems
• Dynamically consistent reduction of logical regulatory graphs
• EVIDENCE OF SCALE-FREE TOPOLOGY IN GENE REGULATORY NETWORK OF HUMAN TISSUES
• Revealing the canalizing structure of Boolean functions: algorithms and applications
• Boolean nested canalizing functions: a comprehensive analysis
• Algebraic Models and Their Use in Systems Biology
• Stability of linear Boolean networks

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