Modeling gene regulatory network motifs using statecharts

BMC Bioinformatics

Research

Manuela Helmer-Citterich¹  Enrico Nardelli²  Fabio Fioravanti³ 

[1] Department of Biology, University of Rome "Tor Vergata", I-00133, Rome, Italy;Department of Mathematics, University of Rome "Tor Vergata", I-00133, Rome, Italy;Department of Sciences, University of Chieti-Pescara "G. D'Annunzio", I-65127, Pescara, Italy;

关键词: Temporal Behavior;    Gene Regulatory Network;    Boolean Network;    Logical Formula;    Feedforward Loop;   

DOI  :  10.1186/1471-2105-13-S4-S20

来源: Springer

【 摘 要 】

BackgroundGene regulatory networks are widely used by biologists to describe the interactions among genes, proteins and other components at the intra-cellular level. Recently, a great effort has been devoted to give gene regulatory networks a formal semantics based on existing computational frameworks.For this purpose, we consider Statecharts, which are a modular, hierarchical and executable formal model widely used to represent software systems. We use Statecharts for modeling small and recurring patterns of interactions in gene regulatory networks, called motifs.ResultsWe present an improved method for modeling gene regulatory network motifs using Statecharts and we describe the successful modeling of several motifs, including those which could not be modeled or whose models could not be distinguished using the method of a previous proposal.We model motifs in an easy and intuitive way by taking advantage of the visual features of Statecharts. Our modeling approach is able to simulate some interesting temporal properties of gene regulatory network motifs: the delay in the activation and the deactivation of the "output" gene in the coherent type-1 feedforward loop, the pulse in the incoherent type-1 feedforward loop, the bistability nature of double positive and double negative feedback loops, the oscillatory behavior of the negative feedback loop, and the "lock-in" effect of positive autoregulation.ConclusionsWe present a Statecharts-based approach for the modeling of gene regulatory network motifs in biological systems. The basic motifs used to build more complex networks (that is, simple regulation, reciprocal regulation, feedback loop, feedforward loop, and autoregulation) can be faithfully described and their temporal dynamics can be analyzed.

【 授权许可】

Unknown   
© Fioravanti et al.; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.