Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, China.
Bioinformatics. 2010 Jan 15;26(2):275-7. doi: 10.1093/bioinformatics/btp634. Epub 2009 Nov 13.
The propagation of perturbations in protein concentration through a protein interaction network (PIN) can shed light on network dynamics and function. In order to facilitate this type of study, PerturbationAnalyzer, which is an open source plugin for Cytoscape, has been developed. PerturbationAnalyzer can be used in manual mode for simulating user-defined perturbations, as well as in batch mode for evaluating network robustness and identifying significant proteins that cause large propagation effects in the PINs when their concentrations are perturbed. Results from PerturbationAnalyzer can be represented in an intuitive and customizable way and can also be exported for further exploration. PerturbationAnalyzer has great potential in mining the design principles of protein networks, and may be a useful tool for identifying drug targets.
PerturbationAnalyzer can be accessed from the Cytoscape web site http://www.cytoscape.org/plugins/index.php or http://biotech.bmi.ac.cn/PerturbationAnalyzer.
Supplementary data are available at Bioinformatics online.
通过蛋白质相互作用网络（PIN）中蛋白质浓度的波动传播，可以揭示网络动态和功能。为了便于进行此类研究，开发了 Cytoscape 的开源插件 PerturbationAnalyzer。PerturbationAnalyzer 既可以用于手动模拟用户定义的扰动，也可以用于批量评估网络鲁棒性，并在扰动 PIN 中蛋白质浓度时识别出导致较大传播效果的重要蛋白质。PerturbationAnalyzer 的结果可以以直观和可定制的方式表示，也可以导出以供进一步探索。PerturbationAnalyzer 在挖掘蛋白质网络设计原则方面具有巨大潜力，可能是识别药物靶点的有用工具。
可以从 Cytoscape 网站 http://www.cytoscape.org/plugins/index.php 或 http://biotech.bmi.ac.cn/PerturbationAnalyzer 访问 PerturbationAnalyzer。
补充数据可在 Bioinformatics 在线获得。
