Journal Article

PerturbationAnalyzer: a tool for investigating the effects of concentration perturbation on protein interaction networks

Fei Li, Peng Li, Wenjian Xu, Yuxing Peng, Xiaochen Bo and Shengqi Wang

in Bioinformatics

Volume 26, issue 2, pages 275-277
Published in print January 2010 | ISSN: 1367-4803
Published online November 2009 | e-ISSN: 1460-2059 | DOI: https://dx.doi.org/10.1093/bioinformatics/btp634
PerturbationAnalyzer: a tool for investigating the effects of concentration perturbation on protein interaction networks

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Summary: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.

Availability:PerturbationAnalyzer can be accessed from the Cytoscape web site http://www.cytoscape.org/plugins/index.php or http://biotech.bmi.ac.cn/PerturbationAnalyzer.

Contact: boxc@bmi.ac.cn; sqwang@bmi.ac.cn

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  1353 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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