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Minimal cut sets in a metabolic network are elementary modes in a dual network

Ballerstein, Kathrin ; von Kamp, Axel ; Klamt, Steffen ; Haus, Utz-Uwe

In: Bioinformatics, 2012, vol. 28, no. 3, p. 381-387

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    Titre
    • Minimal cut sets in a metabolic network are elementary modes in a dual network
    Auteur
    • Ballerstein, Kathrin. Institute for Operations Research, Department of Mathematics, ETH Zürich, Rämistrasse 101, 8092 Zürich, Switzerland and Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany
    • von Kamp, Axel. Institute for Operations Research, Department of Mathematics, ETH Zürich, Rämistrasse 101, 8092 Zürich, Switzerland and Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany
    • Klamt, Steffen. Institute for Operations Research, Department of Mathematics, ETH Zürich, Rämistrasse 101, 8092 Zürich, Switzerland and Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany
    • Haus, Utz-Uwe. Institute for Operations Research, Department of Mathematics, ETH Zürich, Rämistrasse 101, 8092 Zürich, Switzerland and Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany
    Type de document
    • Postprint
    Identifiant OAI-PMH
    • oai:doc.rero.ch:298744
    Summary
    Motivation: Elementary modes (EMs) and minimal cut sets (MCSs) provide important techniques for metabolic network modeling. Whereas EMs describe minimal subnetworks that can function in steady state, MCSs are sets of reactions whose removal will disable certain network functions. Effective algorithms were developed for EM computation while calculation of MCSs is typically addressed by indirect methods requiring the computation of EMs as initial step. Results: In this contribution, we provide a method that determines MCSs directly without calculating the EMs. We introduce a duality framework for metabolic networks where the enumeration of MCSs in the original network is reduced to identifying the EMs in a dual network. As a further extension, we propose a generalization of MCSs in metabolic networks by allowing the combination of inhomogeneous constraints on reaction rates. This framework provides a promising tool to open the concept of EMs and MCSs to a wider class of applications. Contact: utz-uwe.haus@math.ethz.ch; klamt@mpi-magdeburg.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online