Causal structure of oscillations in gene regulatory networks: Boolean analysis of ordinary differential equation attractors.

Journal Article (Journal Article)

A common approach to the modeling of gene regulatory networks is to represent activating or repressing interactions using ordinary differential equations for target gene concentrations that include Hill function dependences on regulator gene concentrations. An alternative formulation represents the same interactions using Boolean logic with time delays associated with each network link. We consider the attractors that emerge from the two types of models in the case of a simple but nontrivial network: a figure-8 network with one positive and one negative feedback loop. We show that the different modeling approaches give rise to the same qualitative set of attractors with the exception of a possible fixed point in the ordinary differential equation model in which concentrations sit at intermediate values. The properties of the attractors are most easily understood from the Boolean perspective, suggesting that time-delay Boolean modeling is a useful tool for understanding the logic of regulatory networks.

Full Text

Duke Authors

Cited Authors

  • Sun, M; Cheng, X; Socolar, JES

Published Date

  • June 2013

Published In

Volume / Issue

  • 23 / 2

Start / End Page

  • 025104 -

PubMed ID

  • 23822502

Pubmed Central ID

  • PMC3689811

Electronic International Standard Serial Number (EISSN)

  • 1089-7682

International Standard Serial Number (ISSN)

  • 1054-1500

Digital Object Identifier (DOI)

  • 10.1063/1.4807733


  • eng