Theocharidis Athanasios, van Dongen Stjin, Enright Anton J, Freeman Tom C
The Roslin Institute, R(D)SVS, University of Edinburgh, Roslin BioCentre, Midlothian, Scotland, UK.
Nat Protoc. 2009;4(10):1535-50. doi: 10.1038/nprot.2009.177. Epub 2009 Oct 1.
Network analysis has an increasing role in our effort to understand the complexity of biological systems. This is because of our ability to generate large data sets, where the interaction or distance between biological components can be either measured experimentally or calculated. Here we describe the use of BioLayout Express(3D), an application that has been specifically designed for the integration, visualization and analysis of large network graphs derived from biological data. We describe the basic functionality of the program and its ability to display and cluster large graphs in two- and three-dimensional space, thereby rendering graphs in a highly interactive format. Although the program supports the import and display of various data formats, we provide a detailed protocol for one of its unique capabilities, the network analysis of gene expression data and a more general guide to the manipulation of graphs generated from various other data types.
网络分析在我们理解生物系统复杂性的努力中发挥着越来越重要的作用。这是因为我们有能力生成大型数据集，其中生物组件之间的相互作用或距离既可以通过实验测量，也可以进行计算。在这里，我们描述了BioLayout Express(3D)的使用，这是一个专门为整合、可视化和分析从生物数据中导出的大型网络图而设计的应用程序。我们描述了该程序的基本功能及其在二维和三维空间中显示和聚类大型图的能力，从而以高度交互式的格式呈现图。虽然该程序支持导入和显示各种数据格式，但我们为其独特功能之一，即基因表达数据的网络分析提供了详细的方案，并为处理从各种其他数据类型生成的图提供了更通用的指南。
