title: PerturbationAnalyzer: a tool for investigating the effects of concentration perturbation on protein interaction networks.
abstract: 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.
  
  
  BACKGROUND
  PerturbationAnalyzer can be accessed from the Cytoscape web site http://www.cytoscape.org/plugins/index.php or http://biotech.bmi.ac.cn/PerturbationAnalyzer.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, China.
authors.forename: Fei
authors.initials: F
authors.lastname: Li
authors.forename: Peng
authors.initials: P
authors.lastname: Li
authors.forename: Wenjian
authors.initials: W
authors.lastname: Xu
authors.forename: Yuxing
authors.initials: Y
authors.lastname: Peng
authors.forename: Xiaochen
authors.initials: X
authors.lastname: Bo
authors.forename: Shengqi
authors.initials: S
authors.lastname: Wang
mesh_terms: D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012984:Software
chemical_list: D011506:Proteins