Capturing the essence of a metabolic network: A flux balance analysis approach |
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Authors: | Ettore Murabito Evangelos Simeonidis Kieran Smallbone Jonathan Swinton |
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Institution: | a Doctoral Training Centre Integrative Systems Biology from Molecules to Life, Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK b School of Chemical Engineering and Analytical Science, The University of Manchester, Sackville Street, Manchester M60 1QD, UK c Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK d School of Mathematics, The University of Manchester, Oxford Road, Manchester M13 9PL, UK e Computational Biology/Advanced Science and Technology Laboratory, AstraZeneca |
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Abstract: | As genome-scale metabolic reconstructions emerge, tools to manage their size and complexity will be increasingly important. Flux balance analysis (FBA) is a constraint-based approach widely used to study the metabolic capabilities of cellular or subcellular systems. FBA problems are highly underdetermined and many different phenotypes can satisfy any set of constraints through which the metabolic system is represented.Two of the main concerns in FBA are exploring the space of solutions for a given metabolic network and finding a specific phenotype which is representative for a given task such as maximal growth rate. Here, we introduce a recursive algorithm suitable for overcoming both of these concerns. The method proposed is able to find the alternate optimal patterns of active reactions of an FBA problem and identify the minimal subnetwork able to perform a specific task as optimally as the whole.Our method represents an alternative to and an extension of other approaches conceived for exploring the space of solutions of an FBA problem. It may also be particularly helpful in defining a scaffold of reactions upon which to build up a dynamic model, when the important pathways of the system have not yet been well-defined. |
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Keywords: | Mixed integer linear programming problem Alternate optimal solutions Alternate optimal patterns Minimal optimal subnetwork Minimal effort principle |
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