Institute for Operations Research, Department of Mathematics, ETH Zürich, Rämistrasse 101, 8092 Zürich, Switzerland.
Bioinformatics. 2012 Feb 1;28(3):381-7. doi: 10.1093/bioinformatics/btr674. Epub 2011 Dec 21.
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.
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.
utz-uwe.haus@math.ethz.ch; klamt@mpi-magdeburg.mpg.de
Supplementary data are available at Bioinformatics online.
基本模式 (EMs) 和最小割集 (MCSs) 为代谢网络建模提供了重要的技术。EMs 描述了可以在稳态下发挥作用的最小子网，而 MCSs 是一组反应，去除这些反应将使某些网络功能失效。已经开发了有效的 EM 计算算法，而 MCS 的计算通常通过需要计算 EM 作为初始步骤的间接方法来解决。
在本研究中，我们提供了一种无需计算 EMs 即可直接确定 MCSs 的方法。我们为代谢网络引入了一个对偶框架，其中原始网络中 MCS 的枚举可以简化为在对偶网络中识别 EMs。作为进一步的扩展，我们通过允许对反应速率施加不均匀的约束，提出了代谢网络中 MCS 的一种推广。该框架为将 EMs 和 MCSs 的概念扩展到更广泛的应用领域提供了一个很有前途的工具。
utz-uwe.haus@math.ethz.ch; klamt@mpi-magdeburg.mpg.de
补充数据可在“Bioinformatics”在线获取。
