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Bioessays. 2010 Mar;32(3):246-56. doi: 10.1002/bies.200900145.

When metabolism meets topology: Reconciling metabolite and reaction networks.

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  • 1Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Spain.


The search for a systems-level picture of metabolism as a web of molecular interactions provides a paradigmatic example of how the methods used to characterize a system can bias the interpretation of its functional meaning. Metabolic maps have been analyzed using novel techniques from network theory, revealing some non-trivial, functionally relevant properties. These include a small-world structure and hierarchical modularity. However, as discussed here, some of these properties might actually result from an inappropriate way of defining network interactions. Starting from the so-called bipartite organization of metabolism, where the two meaningful subsets (reactions and metabolites) are considered, most current works use only one of the subsets by means of so-called graph projections. Unfortunately, projected graphs often ignore relevant biological and chemical constraints, thus leading to statistical artifacts. Some of these drawbacks and alternative approaches need to be properly addressed.

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