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A Practical Protocol for Integration of Transcriptomics Data into Genome-Scale Metabolic Reconstructions

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Hydrocarbon and Lipid Microbiology Protocols

Part of the book series: Springer Protocols Handbooks ((SPH))

Abstract

In recent years, an avalanche of data in the form of the so-called omics has been generated in biological sciences. Nevertheless, the effective use of this huge volume of data is challenging from a purely mathematical and statistical point of view, and integrative approaches are becoming a necessity. Genome-scale metabolic models offer an unprecedented chance to integrate and contextualise, in the correct biological context, this large amount of omics data being generated. This chapter provides a step-by-step protocol for the integration of transcriptomics data in genome-scale metabolic models by constructing condition-specific bacterial models. Subsequently, they are used to increase the accuracy of the in silico predictions in terms of metabolic flux prediction and for the better contextualisation of the transcriptomics data in the correct biological context. Two models environmental bacterial such as Pseudomonas putida KT2440 and Synechocystis sp. PCC 8063 and their corresponding GEMs are used here for such proposes.

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Acknowledgements

The authors would like to thank C. Herencias for testing the protocol and valuable discussion.

The research leading to these results has received funding from the Ministry of Economy and Competitiveness of Spain Grant BIO2012-39501, European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement no. 311815 (SYNPOL project, http://www.synpol.org/) and European Union’s H2020 ERAIB LigBio project (PCIN-2014-113).

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Authors and Affiliations

  1. Department of Environmental Biology, Centro de Investigaciones Biológicas-CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain

    Juan Nogales & Lucía Agudo

Authors
  1. Juan Nogales
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  2. Lucía Agudo
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Corresponding author

Correspondence to Juan Nogales .

Editor information

Editors and Affiliations

  1. University of Essex Dept. Biological Sciences, Colchester, Essex, United Kingdom

    Terry J. McGenity

  2. Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany

    Kenneth N. Timmis

  3. Department of Biology, University of the Balearic Islands and Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Palma de Mallorca, Spain

    Balbina Nogales

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© 2015 Springer-Verlag Berlin Heidelberg

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Nogales, J., Agudo, L. (2015). A Practical Protocol for Integration of Transcriptomics Data into Genome-Scale Metabolic Reconstructions. In: McGenity, T., Timmis, K., Nogales, B. (eds) Hydrocarbon and Lipid Microbiology Protocols . Springer Protocols Handbooks. Springer, Berlin, Heidelberg. https://doi.org/10.1007/8623_2015_98

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  • DOI: https://doi.org/10.1007/8623_2015_98

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-662-50430-7

  • Online ISBN: 978-3-662-50432-1

  • eBook Packages: Springer Protocols

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