Wiredja Danica, Bebek Gurkan
Systems Biology and Bioinformatics Graduate Program, Case Western Reserve University School of Medicine, Cleveland, OH, 44116, USA.
Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH, 44116, USA.
Methods Mol Biol. 2017;1666:539-556. doi: 10.1007/978-1-4939-7274-6_27.
In this chapter, we introduce interaction networks by describing how they are generated, where they are stored, and how they are shared. We focus on publicly available interaction networks and describe a simple way of utilizing these resources. This chapter features two case studies, both of which utilize Cytoscape, an open source and user-friendly network visualization and analysis tool. In the first example, we demonstrate the basic functionalities of Cytoscape by building an interaction network from a publicly available database, analyzing its topological features, and performing gene ontology enrichment. For the second section, we constructed a network from scratch starting with an experimental gene expression dataset. From there, we implement more advanced visual annotations of the network and perform subnetwork enrichment. The methods described are applicable to larger networks that can be collected from various resources.
在本章中，我们通过描述相互作用网络是如何生成的、存储在何处以及如何共享来介绍它们。我们专注于公开可用的相互作用网络，并描述一种利用这些资源的简单方法。本章有两个案例研究，两者都使用了Cytoscape，这是一个开源且用户友好的网络可视化和分析工具。在第一个例子中，我们通过从一个公开可用的数据库构建相互作用网络、分析其拓扑特征以及进行基因本体富集来展示Cytoscape的基本功能。在第二部分中，我们从一个实验性基因表达数据集开始从头构建一个网络。从那里，我们对网络实施更高级的视觉注释并进行子网富集。所描述的方法适用于可以从各种资源收集的更大的网络。
