Mathematical Modelling of Gene Regulatory Networks

Abstract

Living cells can be observed as complex dynamical systems that are constantly remodelling themselves as response to changes in their environment (Zak et al., 2005). The cell metabolism includes number of reactions and products of reactions which interact forming a metabolic network. Due to the fact that large amount of date about processes in living cells are being collected every day, it become necessary to use computers for data processing and analysis. Introducing computer technologies into biology new discipline has been develop, systems biology or computational biology. The aim of system biology is describing and understanding how parts of organism interact in one complex system ; systems biology aims to develop mathematical model of biological systems by integrating experimental and theoretical techniques (Hecker et al., 2009, Albert, 2004). Systems biology studies biological systems by systematically perturbating them (biologically, genetically or chemically) monitoring the genes, proteins and informational pathway response (Strizh et al., 2007). Progress in molecular biology led to development of complete maps of genomes of many organisms ; it is also possible to identify and classify proteins. Although the number of completely sequenced genomes is mounting rapidly, our knowledge of transcription regulation is limited to a few model organisms (Janga and Collado-Vides, 2007). The interactive regulation of genes, working together to create gene networks has been considered the origin of many functions of organism (Mochizuki, 2008). According to Bruggeman and Westerholl, a complete systems biology approach requires (i) characterisation of organism molecular composition, (ii) components dynamics (spatial and temporal) and (iii) detail analysis of molecular response to internal and external stimuli. All these facts are included in development of gene regulatory network. In this chapter the theory of gene regulatory networks will be presented. The chapter will start with ideas how gene regulatory networks are constructed. There will be data on different types of gene regulatory networks and approaches for modeling those systems. This chapter will try to explain why is the modeling of complex regulatory networks important for genetic engineering and how can the mathematical analysis of gene regulatory networks be used for genetic engineering experiments planning and results interpretation.