Modular decomposition of metabolic systems via null-space analysis
Modular decomposition of metabolic systems via null-space analysis
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DOI：
10.1016/j.jtbi.2007.08.005
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发表时间：
2007-12-21
影响因子：
2
通讯作者：
Fell, David A.
中科院分区：
文献类型：
--
作者：
Poolman, Mark G.;Sebu, Cristiana;Fell, David A.
我们描述了一种方法，通过该方法，代谢系统中的反应可以分层地分组到模块组中以形成代谢反应树。与以前的方法相比，这里描述的方法考虑到这样一个事实，即在一个可行的网络，反应必须能够维持一个稳态flux.In为了实现这种分解，我们引入了一个新的概念-反应相关系数，φ和显示，这是一个逻辑扩展的概念酶（或反应）子集。除了它们的应用模块分解，反应相关系数有一些其他有趣的属性，包括一个方便的手段，用于识别断开的子网络在一个系统和潜在的应用代谢engineering.The方法计算反应相关系数从零空间的化学计量矩阵的正交基。我们表明，反应相关系数是唯一定义的，即使零空间的基础是不是。一旦一套完整的反应相关系数计算，代谢反应树可以通过标准的编程技术的应用程序来确定。反应相关系数的计算，以及随后的代谢反应树的构建对于使用商品台式PC的基因组规模模型是容易实现的。(c)2007爱思唯尔有限公司保留所有权利。
We describe a method by which the reactions in a metabolic system may be grouped hierarchically into sets of modules to form a metabolic reaction tree. In contrast to previous approaches, the method described here takes into account the fact that, in a viable network, reactions must be capable of sustaining a steady-state flux.In order to achieve this decomposition we introduce a new concept-the reaction correlation coefficient, phi and show that this is a logical extension of the concept of enzyme (or reaction) subsets. In addition to their application to modular decomposition, reaction correlation coefficients have a umber of other interesting properties, including a convenient means for identifying disconnected subnetworks in a system and potential applications to metabolic engineering.The method computes reaction correlation coefficients from an orthonormal basis of the null-space of the stoichiometry matrix. We show that reaction correlation coefficients are uniquely defined, even though the basis of the null-space is not.Once a complete set of reaction correlation coefficients is calculated, a metabolic reaction tree can be determined through the application of standard programming techniques. Computation of the reaction correlation coefficients, and the Subsequent construction of the metabolic reaction tree is readily achievable for genorne-scale models using a commodity desk-top PC. (c) 2007 Elsevier Ltd. All rights reserved.