PerturbationAnalyzer: A tool for investigating the effects of concentration perturbation on protein interaction networks. Bioinformatics (Oxford, England) [Bioinformatics] Journal article | | Title | PerturbationAnalyzer: A tool for investigating the effects of concentration perturbation on protein interaction networks. | | Author(s) | Li F, Li P, Xu W, Peng Y, Bo X, Wang S | | Institution | Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, China. | | Source | Bioinformatics 2009 Nov 13. | | Abstract | SUMMARY: The propagation of perturbations in protein concentration through a protein interaction network 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 website http://www.cytoscape.org/plugins/index.php or website http://biotech.bmi.ac.cn/PerturbationAnalyzer.
CONTACT: boxc@bmi.ac.cn; sqwang@bmi.ac.cn. | | Language | ENG | | Pub Type(s) | JOURNAL ARTICLE
| | PubMed ID | 19914922 |
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