Lacroix Vincent, Fernandes Cristina G, Sagot Marie-France
Equipe BAOBAB, Laboratoire de Biométrie et Biologie Evolutive, CNRS, Univ. Lyon, Villeurbanne, France.
IEEE/ACM Trans Comput Biol Bioinform. 2006 Oct-Dec;3(4):360-8. doi: 10.1109/TCBB.2006.55.
The classic view of metabolism as a collection of metabolic pathways is being questioned with the currently available possibility of studying whole networks. Novel ways of decomposing the network into modules and motifs that could be considered as the building blocks of a network are being suggested. In this work, we introduce a new definition of motif in the context of metabolic networks. Unlike in previous works on (other) biochemical networks, this definition is not based only on topological features. We propose instead to use an alternative definition based on the functional nature of the components that form the motif, which we call a reaction motif. After introducing a formal framework motivated by biological considerations, we present complexity results on the problem of searching for all occurrences of a reaction motif in a network and introduce an algorithm that is fast in practice in most situations. We then show an initial application to the study of pathway evolution. Finally, we give some general features of the observed number of occurrences in order to highlight some structural features of metabolic networks.
将新陈代谢视为一系列代谢途径的经典观点正受到质疑，因为目前有研究整个网络的可能性。人们提出了将网络分解为模块和基序的新方法，这些模块和基序可被视为网络的构建块。在这项工作中，我们在代谢网络的背景下引入了基序的新定义。与之前关于（其他）生化网络的工作不同，这个定义不仅基于拓扑特征。相反，我们建议使用基于构成基序的组件功能性质的替代定义，我们称之为反应基序。在引入一个受生物学考虑驱动的形式框架后，我们给出了在网络中搜索反应基序所有出现情况问题的复杂性结果，并介绍了一种在大多数情况下实际运行速度很快的算法。然后，我们展示了其在途径进化研究中的初步应用。最后，我们给出了观察到的出现次数的一些一般特征，以突出代谢网络的一些结构特征。
