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Qualitative modelling of metabolic networks

Abstract : Global and untargeted approaches such as metabolomics require analysis of experimental data with no assumption regarding the organism's functions affected by any environmental or genetic stress. From a metabolism perspective, it means that the metabolic shift induced by the studied perturbation may span several pathways. The challenge is then to incorporate and analyze simultaneously all the metabolic reactions. This is achieved by using genome-scale metabolic networks since they gather in a single model all the anabolic and catabolic reactions a cell or an organism can perform. This information is generally retrieved by processing genome sequences and applying validation methods. In this chapter, we will discuss how they are built and raise some issues on databases and network exchanges between different platforms. Then, we will show how graph modelling can be used to model and process this qualitative information. In particular, we will focus on the way to identify reaction paths between metabolites and how it can be used to create sub-networks based on metabolomics data. Finally, since these networks often contain thousands of reactions and metabolites, we will illustrate how visualization can be used to enhance this qualitative mining of metabolism.
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Submitted on : Friday, June 5, 2020 - 10:27:09 PM
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Fabien Jourdan. Qualitative modelling of metabolic networks. Metabolomics coming of age with its technological diversity, 67, 2013, Advances in Botanical Research, ⟨10.1016/B978-0-12-397922-3.00012-5⟩. ⟨hal-02803214⟩



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