Journal of Mathematical Biology

, Volume 69, Issue 5, pp 1151–1179 | Cite as

Flux modules in metabolic networks

Article

Abstract

The huge number of elementary flux modes in genome-scale metabolic networks makes analysis based on elementary flux modes intrinsically difficult. However, it has been shown that the elementary flux modes with optimal yield often contain highly redundant information. The set of optimal-yield elementary flux modes can be compressed using modules. Up to now, this compression was only possible by first enumerating the whole set of all optimal-yield elementary flux modes. We present a direct method for computing modules of the thermodynamically constrained optimal flux space of a metabolic network. This method can be used to decompose the set of optimal-yield elementary flux modes in a modular way and to speed up their computation. In addition, it provides a new form of coupling information that is not obtained by classical flux coupling analysis. We illustrate our approach on a set of model organisms.

Keywords

Metabolic network Flux balance analysis Elementary flux modes Modules 

Mathematics Subject Classification (2000)

92C42 52B15 90C35 

Notes

Acknowledgments

We thank Leen Stougie, who presented this problem on the ENUMEX Summerschool (Enumeration Algorithms & Exact Methods For Exponential Problems in Computational Biology).

Funding:This work was funded by the Berlin Mathematical School in terms of a PhD stipend.

Supplementary material

285_2013_731_MOESM1_ESM.pdf (132 kb)
Supplementary material 1 (pdf 132 KB)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  1. 1.Department of Mathematics and Computer ScienceFreie Universität BerlinBerlinGermany
  2. 2.International Max Planck Research School for Computational Biology and Scientific Computing (IMPRS-CBSC)Max Planck Institute for Molecular GeneticsBerlinGermany
  3. 3.Berlin Mathematical School (BMS)BerlinGermany
  4. 4.DFG-Research Center MatheonBerlinGermany

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