Faust Karoline, van Helden Jacques
Department of Applied Biological Sciences (DBIT), Vrije Universiteit Brussel, Bruxelles, Belgium.
Methods Mol Biol. 2012;804:107-30. doi: 10.1007/978-1-61779-361-5_7.
Various methods result in groups of functionally related genes obtained from genomes (operons, regulons, syntheny groups, and phylogenetic profiles), transcriptomes (co-expression groups) and proteomes (modules of interacting proteins). When such groups contain two or more enzyme-coding genes, graph analysis methods can be applied to extract a metabolic pathway that interconnects them. We describe here the way to use the Pathway extraction tool available on the NeAT Web server ( http://rsat.ulb.ac.be/neat/ ) to piece together the metabolic pathway from a group of associated, enzyme-coding genes. The tool identifies the reactions that can be catalyzed by the products of the query genes (seed reactions), and applies sub-graph extraction algorithms to extract from a metabolic network a sub-network that connects the seed reactions. This sub-network represents the predicted metabolic pathway. We describe here the pathway prediction process in a step-by-step way, give hints about the main parametric choices, and illustrate how this tool can be used to extract metabolic pathways from bacterial genomes, on the basis of two study cases: the isoleucine-valine operon in Escherichia coli and a predicted operon in Cupriavidus (Ralstonia) metallidurans.
多种方法可从基因组（操纵子、调控子、同线性组和系统发育谱）、转录组（共表达组）和蛋白质组（相互作用蛋白质模块）中获得功能相关的基因群。当这些基因群包含两个或更多酶编码基因时，可应用图分析方法来提取将它们相互连接的代谢途径。我们在此描述使用NeAT网络服务器（http://rsat.ulb.ac.be/neat/ ）上的途径提取工具，从一组相关的酶编码基因拼凑代谢途径的方法。该工具识别可由查询基因产物催化的反应（种子反应），并应用子图提取算法从代谢网络中提取连接种子反应的子网络。这个子网络代表预测的代谢途径。我们在此逐步描述途径预测过程，给出关于主要参数选择的提示，并基于两个研究案例说明如何使用该工具从细菌基因组中提取代谢途径：大肠杆菌中的异亮氨酸 - 缬氨酸操纵子和金属抗性贪铜菌（雷尔氏菌属）中的一个预测操纵子。
