一种由代谢方程构建网络的方法及其实现  

A method for constructing networks from metabolic equations and its procedural steps

作　　者：何胜[1] 吴访升[1] 潘瑜[1] 徐明亮[2] 杨莉[1] 李炜疆[3] 

机构地区：[1]江苏技术师范学院计算机科学与工程学院,江苏常州213001 [2]无锡城市职业技术学院电子信息系,江苏无锡214063 [3]江南大学生物工程学院,江苏无锡214122

出　　处：《计算机与应用化学》2011年第9期1199-1202,共4页Computers and Applied Chemistry

基　　金：江南大学工业生物技术教育部重点实验室开放课题(KLIB-KF200903);江苏技术师范学院科研启动基金项目(KYY10059)

摘　　要：代谢网络的拓扑结构分析和可视化是系统生物学研究的热点。如何自动合理地由数量众多的代谢方程构建代谢网络是研究者首先面临的问题。基于二部图模型,采用"节点唯一化"和"忽略高度节点"策略,提出一种由代谢方程直接构建代谢网络的方法,并给出MATLAB实现步骤,最后使用生物网络模拟软件可视化生成的代谢网络,结果表明这种方法能用来构建复杂代谢网络,并具有较好展现网络模块和拓扑结构的特点,适用于由大量代谢反应方程自动构建复杂代谢网络的一般应用需求。该方法的MATLAB源码和说明文档可以通过http://bioinf.jiangnan.edu.cn/在线获得。It is a challenge for biological researchers to understand complex cellular metabolic processes. Metabolic processes are usually described by large numbers of metabolic equations which are included in the biological models and database. In systems biology, one of important methods of studying cellular metabolic processes is to visualize the metabolic networks constructed by these metabolic equations in which metabolites and enzymes are treated as nodes and the relations between them as edges, therefore, the first problem is to construct metabolic networks from numerous metabolic equations automatically and reasonably. MATLAB is a popular numerical analysis tool due to its powerful numerical analysis functions and strong matrix computation abilities. Because networks can be described conveniently by matrix, MATLAB can be used to analyze and construct metabolic networks. Based on bipartite model and strategies of＂unique nodes＂ and ＂ignoring high degree nodes＂, a method of construction metabolic networks from metabolic equations was proposed and the procedural steps of MATLAB were given. To check the above strategies, three sets of metabolic equations of Pseudomonas putida KT2440 were selected to construct metabolic network according to the above methods. The output constructed networks were visualized by simulator software of biological network. The result shows this method can be used to construct complex metabolic networks and display the characteristics of network module and topology. This method is suitable for general requirements of construction complex metabolic networks from numerous metabolic equations. The MATLAB scripts and help documentation for our methods are available online at http ：//bioinf.j iangnan.edu.cn/.

关 键 词：代谢方程 代谢网络 可视化 

分 类 号：Q811.4[生物学—生物工程]