network-based approaches for linking metabolism with environment基于网络的方法连接新陈代谢和环境.pdfVIP

Minireview NNeettwwoorrkk--bbaasseedd aapppprrooaacchheess ffoorr lliinnkkiinngg mmeettaabboolliissmm wwiitthh eennvviirroonnmmeenntt Sarath Chandra Janga and M Madan Babu Address: MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK. Correspondence: Sarath Chandra Janga. Email: sarath@mrc-lmb.cam.ac.uk Published: 24 November2008 Genome BBiioollooggyy 2008, 99::239 (doi:10.1186/gb-2008-9-11-239) The electronic version of this article is the complete one and can be found online at /2008/9/11/239 © 2008 BioMed Central Ltd AAbbssttrraacctt Progress in the reconstruction of genome-wide metabolic maps has led to the development of network-based computational approaches for linking an organism with its biochemical habitat. The sequential nature of the reactions in metabolic pathways data from a large number of bacterial metabolic networks, means that they can be modeled in the form of a graph Kreimer et al. address the question of how the topologies of (network) of enzymes and chemical transformations, and the metabolic networks from different species reflect both network theory can be used to represent and understand genome size and the diversity of environmental conditions metabolism [1,2]. The connected collection of metabolic the species would encounter. Borenstein et al. set out to pathways, describing the set of all enzymatic interc- identify the ‘seed set’ - that set of small molecules that are onversions of one small molecule into another, is defined as absolutely needed from the external environment - of each the metabolic network of an organism (Figure 1a).