Quintero Andrés, Ramírez Jorge, Leal Luis Guillermo, López-Kleine Liliana
Universidad Nacional de Colombia, Department of Biology, Master Student, Universidad Nacional de Colombia-Sede Bogotá
Universidad Nacional de Colombia, School of Mathematics, Associate Professor, Universidad Nacional de Colombia-Sede Medellín.
Curr Genomics. 2014 Oct;15(5):400-7. doi: 10.2174/1389202915666140807004909.
Relationships between genes are best represented using networks constructed from information of different types, with metabolic information being the most valuable and widely used for genetic network reconstruction. Other types of information are usually also available, and it would be desirable to systematically include them in algorithms for network reconstruction. Here, we present an algorithm to construct a global metabolic network that uses all available enzymatic and metabolic information about the organism. We construct a global enzymatic network (GEN) with a total of 4226 nodes (EC numbers) and 42723 edges representing all known metabolic reactions. As an example we use microarray data for Arabidopsis thaliana and combine it with the metabolic network constructing a final gene interaction network for this organism with 8212 nodes (genes) and 4606,901 edges. All scripts are available to be used for any organism for which genomic data is available.
基因之间的关系最好用基于不同类型信息构建的网络来表示，其中代谢信息最有价值且在基因网络重建中应用最为广泛。通常也可获取其他类型的信息，将它们系统地纳入网络重建算法会很有必要。在此，我们提出一种算法来构建一个利用关于该生物体所有可用酶促和代谢信息的全局代谢网络。我们构建了一个全局酶网络（GEN），它共有4226个节点（酶学委员会编号）和42723条边，代表了所有已知的代谢反应。作为示例，我们使用拟南芥的微阵列数据，并将其与代谢网络相结合，构建了该生物体的最终基因相互作用网络，该网络有8212个节点（基因）和4606901条边。所有脚本可供任何有基因组数据的生物体使用。
