Integration of biological networks and gene expression data using Cytoscape
Integration of biological networks and gene expression data using Cytoscape
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DOI：
10.1038/nprot.2007.324
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发表时间：
2007-01-01
期刊：
影响因子：
14.8
通讯作者：
Bader, Gary D.
中科院分区：
文献类型：
--
作者：
Cline, Melissa S.;Smoot, Michael;Bader, Gary D.
Cytoscape是一个用于可视化、建模和分析分子及基因相互作用网络的免费软件包。本方案阐述了如何在感兴趣基因的相互作用网络背景下，使用Cytoscape分析mRNA表达谱以及其他功能基因组学和蛋白质组学实验的结果。描述了五个主要步骤：（i）获取基因或蛋白质网络；（ii）使用布局算法展示网络；（iii）与基因表达及其他功能属性整合；（iv）识别假定的复合物和功能模块；（v）识别网络中富集的基因本体论注释。这些步骤提供了Cytoscape所进行分析类型的广泛示例。
Cytoscape is a free software package for visualizing, modeling and analyzing molecular and genetic interaction networks. This protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and proteomics experiments, in the context of an interaction network obtained for genes of interest. Five major steps are described: (i) obtaining a gene or protein network, (ii) displaying the network using layout algorithms, (iii) integrating with gene expression and other functional attributes, (iv) identifying putative complexes and functional modules and (v) identifying enriched Gene Ontology annotations in the network. These steps provide a broad sample of the types of analyses performed by Cytoscape.