A circuit-preserving mapping from multilevel to Boolean dynamics. 2018

Adrien Fauré, and Shizuo Kaji
Department of Physics and Information Science, Yamaguchi University, 1677-1, Yoshida, Yamaguchi 753-8512, Japan. Electronic address: afaure@yamaguchi-u.ac.jp.

Many discrete models of biological networks rely exclusively on Boolean variables and many tools and theorems are available for analysis of strictly Boolean models. However, multilevel variables are often required to account for threshold effects, in which knowledge of the Boolean case does not generalise straightforwardly. This motivated the development of conversion methods for multilevel to Boolean models. In particular, Van Ham's method has been shown to yield a one-to-one, neighbour and regulation preserving dynamics, making it the de facto standard approach to the problem. However, Van Ham's method has several drawbacks: most notably, it introduces vast regions of "non-admissible" states that have no counterpart in the multilevel, original model. This raises special difficulties for the analysis of interaction between variables and circuit functionality, which is believed to be central to the understanding of dynamic properties of logical models. Here, we propose a new multilevel to Boolean conversion method, with software implementation. Contrary to Van Ham's, our method doesn't yield a one-to-one transposition of multilevel trajectories; however, it maps each and every Boolean state to a specific multilevel state, thus getting rid of the non-admissible regions and, at the expense of (apparently) more complicated, "parallel" trajectories. One of the prominent features of our method is that it preserves dynamics and interaction of variables in a certain manner. As a demonstration of the usability of our method, we apply it to construct a new Boolean counter-example to the well-known conjecture that a local negative circuit is necessary to generate sustained oscillations. This result illustrates the general relevance of our method for the study of multilevel logical models.

UI MeSH Term Description Entries
D008954 Models, Biological Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment. Biological Model,Biological Models,Model, Biological,Models, Biologic,Biologic Model,Biologic Models,Model, Biologic
D000465 Algorithms A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task. Algorithm
D001683 Biological Clocks The physiological mechanisms that govern the rhythmic occurrence of certain biochemical, physiological, and behavioral phenomena. Biological Oscillators,Oscillators, Endogenous,Pacemakers, Biological,Biologic Clock,Biologic Oscillator,Biological Pacemakers,Clock, Biologic,Clocks, Biological,Oscillator, Biologic,Oscillators, Biological,Pacemaker, Biologic,Pacemakers, Biologic,Biologic Clocks,Biologic Oscillators,Biologic Pacemaker,Biologic Pacemakers,Biological Clock,Biological Oscillator,Biological Pacemaker,Clock, Biological,Clocks, Biologic,Endogenous Oscillator,Endogenous Oscillators,Oscillator, Biological,Oscillator, Endogenous,Oscillators, Biologic,Pacemaker, Biological
D014157 Transcription Factors Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process. Transcription Factor,Factor, Transcription,Factors, Transcription
D053263 Gene Regulatory Networks Interacting DNA-encoded regulatory subsystems in the GENOME that coordinate input from activator and repressor TRANSCRIPTION FACTORS during development, cell differentiation, or in response to environmental cues. The networks function to ultimately specify expression of particular sets of GENES for specific conditions, times, or locations. Gene Circuits,Gene Modules,Gene Networks,Transcriptional Networks,Gene Module,Circuit, Gene,Circuits, Gene,Gene Circuit,Gene Network,Gene Regulatory Network,Module, Gene,Modules, Gene,Network, Gene,Network, Gene Regulatory,Network, Transcriptional,Networks, Gene,Networks, Gene Regulatory,Networks, Transcriptional,Regulatory Network, Gene,Regulatory Networks, Gene,Transcriptional Network

Related Publications

Adrien Fauré, and Shizuo Kaji
February 2011, Journal of theoretical biology,
Adrien Fauré, and Shizuo Kaji
September 2012, Physical review. E, Statistical, nonlinear, and soft matter physics,
Adrien Fauré, and Shizuo Kaji
October 2018, Chaos (Woodbury, N.Y.),
Adrien Fauré, and Shizuo Kaji
March 2022, eLife,
Adrien Fauré, and Shizuo Kaji
December 2021, Physical review. E,
Adrien Fauré, and Shizuo Kaji
June 2013, Bulletin of mathematical biology,
Adrien Fauré, and Shizuo Kaji
August 2008, Bioinformatics (Oxford, England),
Adrien Fauré, and Shizuo Kaji
January 2021, Frontiers in systems neuroscience,
Adrien Fauré, and Shizuo Kaji
January 2005, Nonlinear dynamics, psychology, and life sciences,
Adrien Fauré, and Shizuo Kaji
December 2014, Optics express,
Copied contents to your clipboard!