Network visualization and analysis of gene expression data using BioLayout Express3D
Network visualization and analysis of gene expression data using BioLayout Express3D
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DOI：
10.1038/nprot.2009.177
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发表时间：
2009-01-01
期刊：
影响因子：
14.8
通讯作者：
Freeman, Tom C.
中科院分区：
文献类型：
--
作者：
Theocharidis, Athanasios;van Dongen, Stjin;Freeman, Tom C.
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，其中生物成分之间的相互作用或距离可以通过实验测量或计算。在这里，我们描述了BioLayout Express（3D）的使用，该应用程序是专门为集成，可视化和分析来自生物数据的大型网络图而设计的。我们描述的程序的基本功能和它的能力，在二维和三维空间中显示和集群的大型图形，从而呈现图形在一个高度互动的格式。虽然该程序支持各种数据格式的导入和显示，但我们为其独特的功能之一提供了详细的协议，即基因表达数据的网络分析，以及从各种其他数据类型生成的图形操作的更一般指南。
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.