Stability and Structural Properties of Gene Regulation Networks with Coregulation Rules
Coregulation of the expression of groups of genes has been extensively demonstrated empirically in bacterial and eukaryotic systems. Such coregulation can arise through the use of shared regulatory motifs, which allow the coordinated expression of modules (and module groups) of functionally related genes across the genome. Coregulation can also arise through the physical association of multi-gene complexes through chromosomal looping, which are then transcribed together. We present a general formalism for modeling coregulation rules in the framework of Random Boolean Networks (RBN), and develop specific models for transcription factor networks with modular structure (including module groups, and multi-input modules (MIM) with autoregulation) and multi-gene complexes (including hierarchical differentiation between multi-gene complex members). We develop a mean-field approach to analyse the stability of large networks incorporating coregulation, and show that autoregulated MIM and hierarchical gene-complex models can achieve greater stability than networks without coregulation whose rules have matching activation frequency. We provide further analysis of the stability of small networks of both kinds through simulations. We also characterize several general properties of the transients and attractors in the hierarchical coregulation model, and show using simulations that the steady-state distribution factorizes hierarchically as a Bayesian network in a Markov Jump Process analogue of the RBN model.
Code (0)
등록된 구현이 없습니다.
Similar Papers 제목 키워드 기반
Dynamics of ERK regulation in the processive limit
We consider a model of extracellular signal-regulated kinase (ERK) regulation by dual-site phosphorylation and dephosphorylation, which exhibits bistability and oscillations, but loses these properties in the limit in wh…
Integrative analysis reveals disrupted pathways regulated by microRNAs in cancer
MicroRNAs (miRNAs) are small endogenous regulatory molecules that modulate gene expression post-transcriptionally. Although differential expression of miRNAs have been implicated in many diseases (including cancers), the…
Dimensionality ReductionPassivity-based power sharing and voltage regulation in DC microgrids with unactuated buses
In this paper, we propose a novel four-stage distributed controller for a DC microgrid that achieves power sharing and average voltage regulation for the voltages at actuated and unactuated buses. The controller is prese…
Functional Characteristics of Gene Expression Motifs with Single and Dual Strategies of Regulation
Transcriptional regulation by transcription factors and post-transcriptional regulation by microRNAs constitute two major modes of regulation of gene expression. While gene expression motifs incorporating solely transcri…
Family of Two Dimensional Transition Metal Dichlorides Fundamental Properties, Structural Defects, and Environmental Stability
A large number of novel two-dimensional (2D) materials are constantly discovered and deposed into the databases. Consolidate implementation of machine learning algorithms and density functional theory (DFT) based predict…