anNET

anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data. Results: We have developed in Matlab a generalized software called ’anNET’ that affords a user-friendly implementation of the NET analysis algorithm. anNET supports the analysis of any metabolic network for which a stoichiometric model can be compiled. The model size can span from a single reaction to a complete genome-wide network reconstruction including compartments. anNET can (i) test quantitative data sets for thermodynamic consistency, (ii) predict metabolite concentrations beyond the actually measured data, (iii) identify putative sites of active regulation in the metabolic reaction network, and (iv) help in localizing errors in data sets that were found to be thermodynamically infeasible. We demonstrate the application of anNET with three published Escherichia coli metabolome data sets. Conclusion: Our user-friendly and generalized implementation of the NET analysis method in the software anNET allows users to rapidly integrate quantitative metabolome data obtained from virtually any organism. We envision that use of anNET in labs working on quantitative metabolomics will provide the systems biology and metabolic engineering communities with a mean to proof the quality of metabolome data sets and with all further benefits of the NET analysis approach.

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References in zbMATH (referenced in 2 articles )

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  1. Hadlich, Frieder; Nöh, Katharina; Wiechert, Wolfgang: Determination of flux directions by thermodynamic network analysis: Computing informative metabolite pools (2011)
  2. Hoppe, Andreas; Hoffmann, Sabrina; Gerasch, Andreas; Gille, Christoph; Holzhütter, Hermann-Georg: FASIMU: flexible software for flux-balance computation series in large metabolic networks (2011) ioport