Bruck József, Ebenhöh Oliver, Heinrich Reinhart
Theoretical Biophysics, Institute of Biology, Humboldt University, Invalidenstr. 42, D-10115 Berlin, Germany.
Genome Inform. 2006;17(1):208-18.
A large scale structural analysis of metabolic networks is presented focusing on neighbourhood relationships between individual reactions. We define two reactions to be neighbored if one of them provides the necessary set of substances for the other to proceed. A method is developed which allows determining all possible neighborhood relationships categorized as interaction patterns. These patterns differ in the types of participating reactions and in the way they share their reactants. The method is applied to a set of 4795 metabolic reactions contained in the KEGG database. We show that from the 1547 theoretically possible types of interactions 282 patterns are found in metabolism. More than 55% of all interactions occur between reactions with at most two reactants on one side. In these interactions only 25 different patterns play a role. We propose to use these neighborhood relationships as a concept of adjacency in large scale graph theoretical analyses of metabolism.
本文提出了一种针对代谢网络的大规模结构分析，重点关注个体反应之间的邻域关系。如果两个反应中的一个为另一个反应的进行提供了必要的物质集合，我们就定义这两个反应为相邻反应。我们开发了一种方法，该方法可以确定所有可能的邻域关系，并将其分类为相互作用模式。这些模式在参与反应的类型以及它们共享反应物的方式上有所不同。该方法应用于KEGG数据库中包含的4795个代谢反应。我们表明，在1547种理论上可能的相互作用类型中，在代谢中发现了282种模式。超过55%的所有相互作用发生在一侧最多有两种反应物的反应之间。在这些相互作用中，只有25种不同的模式起作用。我们建议在代谢的大规模图论分析中，将这些邻域关系用作邻接概念。
