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Integration of Proteomic and Metabolomic Profiling as well as Metabolic Modeling for the Functional Analysis of Metabolic Networks

Part of the Methods in Molecular Biology book series (MIMB,volume 694)

Abstract

The integrated analysis of different omics-level data sets is most naturally performed in the context of common process or pathway association. In this chapter, the two basic approaches for a metabolic pathway-centric integration of proteomics and metabolomics data are described: the knowledge-based approach relying on existing metabolic pathway information, and a data-driven approach that aims to deduce functional (pathway) associations directly from the data. Relevant algorithmic approaches for the generation of metabolic networks of model organisms, their functional analysis, database resources, visualization and analysis tools will be described. The use of proteomics data in the process of metabolic network reconstruction will be discussed.

Key words

  • Network reconstruction
  • Genome annotation
  • Metabolic modeling
  • Network expansion
  • Flux balance analysis
  • Expression analysis
  • Time-series data analysis
  • Granger causality
  • Systems biology

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Acknowledgements

This work was supported by BMBF-funded GoFORSYS systems biology project. We wish to thank Falk Schreiber for generously providing us with Fig. 2.

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May, P., Christian, N., Ebenhöh, O., Weckwerth, W., Walther, D. (2011). Integration of Proteomic and Metabolomic Profiling as well as Metabolic Modeling for the Functional Analysis of Metabolic Networks. In: Wu, C., Chen, C. (eds) Bioinformatics for Comparative Proteomics. Methods in Molecular Biology, vol 694. Humana Press. https://doi.org/10.1007/978-1-60761-977-2_21

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  • DOI: https://doi.org/10.1007/978-1-60761-977-2_21

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