Reconstruction and structural analysis of metabolic and regulatory networks

Abstract

Networks of interacting cellular components carry out the essential functions in living cells. Therefore, understanding the evolution and design principles of such complex networks is a central issue of systems biology. In recent years, structural analysis methods based on graph theory have revealed several intriguing features of such networks. In this chapter, we describe some of these structural analysis methods and show their application in analysis of biological networks, specifically metabolic and transcriptional regulatory networks (TRNs). We first explain the methods used for reconstruction of biological networks, and then compare the pros and cons of the different methods. It will be shown how graph theory-based methods can help to find the organization principle(s) of the networks, such as the power law degree distribution, the bow-tie connectivity structure, etc. Furthermore, we present an integrated network that includes the metabolite-protein (transcription factor) interaction to link the regulatory network with the metabolic network. This integrated network can provide more insights into the interaction patterns of cellular regulation. © 2007 Humana Press Inc.