Random Boolean Network Models and the Yeast Transcriptional Network

Abstract

The recently measured yeast transcriptional network is analyzed in terms of simplified Boolean network models, with the aim of determining feasible rule structures, given the requirement of stable solutions of the generated Boolean networks. We find that for ensembles of generated models, those with canalyzing Boolean rules are remarkably stable, whereas those with random Boolean rules are only marginally stable. Furthermore, substantial parts of the generated networks are frozen, in the sense that they reach the same state regardless of initial state. Thus, our ensemble approach suggests that the yeast network shows highly ordered dynamics.

23 pages, 5 figures

Cited by in corpus (93)

• Structure and dynamics of molecular networks: A novel paradigm of drug discovery. A comprehensive review
• Colloquium: Criticality and dynamical scaling in living systems
• Genetic networks with canalyzing Boolean rules are always stable
• Number and length of attractors in a critical Kauffman model with connectivity one
• Topology of biological networks and reliability of information processing
• Logic and connectivity jointly determine criticality in biological gene regulatory networks
• Control of complex networks requires both structure and dynamics
• The dynamics of critical Kauffman networks under asynchronous stochastic update
• Critical Networks Exhibit Maximal Information Diversity in Structure-Dynamics Relationships
• Canalizing Kauffman networks: non-ergodicity and its effect on their critical behavior
• Identification of control targets in Boolean molecular network models via computational algebra
• Boolean nested canalizing functions: a comprehensive analysis
• Relative Stability of Network States in Boolean Network Models of Gene Regulation in Development
• A meta-analysis of Boolean network models reveals design principles of gene regulatory networks
• Canalization and control in automata networks: body segmentation in Drosophila melanogaster
• On the number of attractors in random Boolean networks
• A Polynomial-Time Algorithm for Solving the Minimal Observability Problem in Conjunctive Boolean Networks
• Scaling in critical random Boolean networks
• Minimal Controllability of Conjunctive Boolean Networks is NP-Complete
• A Model of Sequential Branching in Hierarchical Cell Fate Determination
• Canalization and Symmetry in Boolean Models for Genetic Regulatory Networks
• Scaling in a general class of critical random Boolean networks
• Regulatory patterns in molecular interaction networks
• On the basic computational structure of gene regulatory networks
• Parameter estimation for Boolean models of biological networks
• The properties of attractors of canalyzing random Boolean networks
• Evolution of Canalizing Boolean Networks
• Molecular Network Control Through Boolean Canalization
• The Influence of Canalization on the Robustness of Boolean Networks
• Entropy of complex relevant components of Boolean networks
• Core percolation and onset of complexity in Boolean networks
• The Number of Multistate Nested Canalyzing Functions
• Experiments on autonomous Boolean networks
• Critical Kauffman networks under deterministic asynchronous update
• Impact of individual nodes in Boolean network dynamics
• The phase diagram of random Boolean networks with nested canalizing functions
• Generic Properties of Random Gene Regulatory Networks
• Kauffman networks with threshold functions
• Dynamical Instability in Boolean Networks as a Percolation Problem
• Relevant components in critical random Boolean networks
• Stability of Boolean networks: The joint effects of topology and update rules
• Computational core and fixed-point organisation in Boolean networks
• Broad edge of chaos in strongly heterogeneous Boolean networks
• Stabilizing Gene Regulatory Networks Through Feedforward Loops
• Stability of Boolean and continuous dynamics
• Robustness, Canalyzing Functions and Systems Design
• Intrinsic noise and deviations from criticality in Boolean gene-regulatory networks
• Finite size corrections to random Boolean networks
• Influence and Dynamic Behavior in Random Boolean Networks
• Representing perturbed dynamics in biological network models
• Boolean networks with veto functions
• Random maps and attractors in random Boolean networks
• Bounds on the Average Sensitivity of Nested Canalizing Functions
• Quantifying the Total Effect of Edge Interventions in Discrete Multistate Networks
• Inferring Biologically Relevant Models: Nested Canalyzing Functions
• Irreversibility in Bacterial Regulatory Networks
• Propagation of external regulation and asynchronous dynamics in random Boolean networks
• Effect of memory in non-Markovian Boolean networks
• Structure-based approach can identify driver nodes in ensembles of biologically-inspired Boolean networks
• Extremely chaotic Boolean networks
• Characterizing short-term stability for Boolean networks over any distribution of transfer functions
• Compensatory interactions to stabilize multiple steady states or mitigate the effects of multiple deregulations in biological networks
• Stability Structures of Conjunctive Boolean Networks
• Asymptotic Behavior of Conjunctive Boolean Networks Over Weakly Connected Digraphs
• Formation of the frozen core in critical Boolean Networks
• Nested canalizing functions minimize sensitivity and simultaneously promote criticality
• Circuits, Attractors and Reachability in Mixed-K Kauffman Networks
• Large attractors in cooperative bi-quadratic Boolean networks. Part II
• Sensitivity and block sensitivity of nested canalyzing function
• Scaling laws in critical random Boolean networks with general in- and out-degree distributions
• Stochastic Modeling and Statistical Inference of Intrinsic Noise in Gene Regulation System via Chemical Master Equation
• Robustness of Transcriptional Regulation in Yeast-like Model Boolean Networks
• Symmetry Properties of Nested Canalyzing Functions
• Universal scaling relation and criticality in metabolism and growth of Escherichia coli
• Stratification and enumeration of Boolean functions by canalizing depth
• On the information-theoretic structure of distributed measurements
• Nested Canalyzing Functions And Their Average Sensitivities
• A network approach to quantifying radiotherapy effect on cancer: Radiosensitive gene group centrality
• Boolean automata isolated cycles and tangential double-cycles dynamics
• Guiding the Self-organization of Random Boolean Networks
• Multi-state Canalyzing Functions over Finite Fields
• Dimension Reduction of Large AND-NOT Network Models
• CABeRNET: a Cytoscape app for Augmented Boolean models of gene Regulatory NETworks
• Anomalies in the transcriptional regulatory network of the yeast Saccharomyces cerevisiae
• The Structure and Dynamics of Gene Regulation Networks
• Study of the structure and dynamics of complex biological networks
• Nested Canalyzing, unate cascade, and polynomial functions
• Computing preimages of Boolean Networks
• Social insect colony as a biological regulatory system: Information flow in dominance networks
• Certificate complexity and symmetry of nested canalizing functions
• Random logic networks: from classical Boolean to quantum dynamics
• Nested canalyzing depth and network stability
• Robustness and fragility of Boolean models for genetic regulatory networks