Cytoscape: A software environment for integrated models of biomolecular interaction networks
Cytoscape: A software environment for integrated models of biomolecular interaction networks
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DOI：
10.1101/gr.1239303
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发表时间：
2003-11-01
期刊：
影响因子：
7
通讯作者：
Ideker, T
中科院分区：
文献类型：
--
作者：
Shannon, P;Markiel, A;Ideker, T
Cytoscape是一个开源软件项目，用于将生物分子相互作用网络与高通量表达数据以及其他分子状态整合到一个统一的概念框架中。尽管适用于任何分子成分和相互作用的系统，但当与蛋白质 - 蛋白质、蛋白质 - DNA和遗传相互作用的大型数据库结合使用时，Cytoscape最为强大，这些数据库对于人类和模式生物越来越容易获取。Cytoscape的软件核心提供了布局和查询网络的基本功能；将网络与表达谱、表型和其他分子状态进行可视化整合；以及将网络与功能注释数据库相链接。核心通过一个简单的插件架构是可扩展的，允许快速开发额外的计算分析和功能。对Cytoscape插件的几个案例研究进行了综述，包括寻找与基因表达变化相关的相互作用途径、对参与细胞从DNA损伤中恢复的蛋白质复合物的研究、对盐杆菌的物理/功能组合相互作用网络的推断，以及一个与详细的随机/动力学基因调控模型的接口。
Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other Molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in Conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to Visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional Computational analyses and features. Several case Studies of Cytoscape plug-ins are Surveyed, including a search for interaction pathways correlating with changes in gene expression, a Study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.