Subnetwork hierarchies of biochemical pathways
Subnetwork hierarchies of biochemical pathways
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DOI：
10.1093/bioinformatics/btg033
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发表时间：
2003-03-01
期刊：
影响因子：
5.8
通讯作者：
Jeong, HW
中科院分区：
文献类型：
--
作者：
Holme, P;Huss, M;Jeong, HW
动机：现代基因组学绘制出的生化网络的巨大性和复杂性要求将其分解为子网络。这种网络可能具有内在的非局部特征，需要在分解过程中考虑全局结构。此外，基本的问题，如在何种程度上的网络（图形理论）可以说是由不同的子networks.Results建立：我们提出了一种方法来分解生化网络到子网络的基础上的全球几何网络。这种方法使我们能够分析生化网络的完整层次组织，并适用于43个生物体的WIT数据库。考虑两种类型的生物化学网络：代谢网络和全细胞网络（也包括例如信息处理）。描述的层次排序的概念和定量的方法进行了讨论。从我们的研究中产生的代谢网络的一般情况是，一些核心集群围绕着最高度连接的物质，这些物质被外壳中的其他物质包围，以及一些其他定义明确的子网络。
Motivation: The vastness and complexity of the biochemical networks that have been mapped out by modern genomics calls for decomposition into subnetworks. Such networks can have inherent non-local features that require the global structure to be taken into account in the decomposition procedure. Furthermore, basic questions such as to what extent the network (graph theoretically) can be said to be built by distinct subnetworks are little studied.Results: We present a method to decompose biochemical networks into subnetworks based on the global geometry of the network. This method enables us to analyze the full hierarchical organization of biochemical networks and is applied to 43 organisms from the WIT database. Two types of biochemical networks are considered: metabolic networks and whole-cellular networks (also including for example information processes). Conceptual and quantitative ways of describing the hierarchical ordering are discussed. The general picture of the metabolic networks arising from our study is that of a few core-clusters centred around the most highly connected substances enclosed by other substances in outer shells, and a few other well-defined subnetworks.