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Identification of a Metabolic Reaction Network from Time-Series Data of Metabolite Concentrations

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  • Kansuporn Sriyudthsak
  • Fumihide Shiraishi
  • Masami Yokota Hirai

Abstract

Recent development of high-throughput analytical techniques has made it possible to qualitatively identify a number of metabolites simultaneously. Correlation and multivariate analyses such as principal component analysis have been widely used to analyse those data and evaluate correlations among the metabolic profiles. However, these analyses cannot simultaneously carry out identification of metabolic reaction networks and prediction of dynamic behaviour of metabolites in the networks. The present study, therefore, proposes a new approach consisting of a combination of statistical technique and mathematical modelling approach to identify and predict a probable metabolic reaction network from time-series data of metabolite concentrations and simultaneously construct its mathematical model. Firstly, regression functions are fitted to experimental data by the locally estimated scatter plot smoothing method. Secondly, the fitted result is analysed by the bivariate Granger causality test to determine which metabolites cause the change in other metabolite concentrations and remove less related metabolites. Thirdly, S-system equations are formed by using the remaining metabolites within the framework of biochemical systems theory. Finally, parameters including rate constants and kinetic orders are estimated by the Levenberg–Marquardt algorithm. The estimation is iterated by setting insignificant kinetic orders at zero, i.e., removing insignificant metabolites. Consequently, a reaction network structure is identified and its mathematical model is obtained. Our approach is validated using a generic inhibition and activation model and its practical application is tested using a simplified model of the glycolysis of Lactococcus lactis MG1363, for which actual time-series data of metabolite concentrations are available. The results indicate the usefulness of our approach and suggest a probable pathway for the production of lactate and acetate. The results also indicate that the approach pinpoints a probable strong inhibition of lactate on the glycolysis pathway.

Suggested Citation

  • Kansuporn Sriyudthsak & Fumihide Shiraishi & Masami Yokota Hirai, 2013. "Identification of a Metabolic Reaction Network from Time-Series Data of Metabolite Concentrations," PLOS ONE, Public Library of Science, vol. 8(1), pages 1-9, January.
    • Handle: RePEc:plo:pone00:0051212
    DOI: 10.1371/journal.pone.0051212
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    References listed on IDEAS

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    2. Granger, C W J, 1969. "Investigating Causal Relations by Econometric Models and Cross-Spectral Methods," Econometrica, Econometric Society, vol. 37(3), pages 424-438, July.
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