title: RCytoscape: tools for exploratory network analysis.
abstract: BACKGROUND
  Biomolecular pathways and networks are dynamic and complex, and the perturbations to them which cause disease are often multiple, heterogeneous and contingent. Pathway and network visualizations, rendered on a computer or published on paper, however, tend to be static, lacking in detail, and ill-equipped to explore the variety and quantities of data available today, and the complex causes we seek to understand.
  
  
  RESULTS
  RCytoscape integrates R (an open-ended programming environment rich in statistical power and data-handling facilities) and Cytoscape (powerful network visualization and analysis software). RCytoscape extends Cytoscape's functionality beyond what is possible with the Cytoscape graphical user interface. To illustrate the power of RCytoscape, a portion of the Glioblastoma multiforme (GBM) data set from the Cancer Genome Atlas (TCGA) is examined. Network visualization reveals previously unreported patterns in the data suggesting heterogeneous signaling mechanisms active in GBM Proneural tumors, with possible clinical relevance.
  
  
  CONCLUSIONS
  Progress in bioinformatics and computational biology depends upon exploratory and confirmatory data analysis, upon inference, and upon modeling. These activities will eventually permit the prediction and control of complex biological systems. Network visualizations--molecular maps--created from an open-ended programming environment rich in statistical power and data-handling facilities, such as RCytoscape, will play an essential role in this progression.
authors.affiliation: Fred Hutchison Cancer Research Institute, Seattle, WA, USA. pshannon@fhcrc.org
authors.forename: Paul T
authors.initials: PT
authors.lastname: Shannon
authors.forename: Mark
authors.initials: M
authors.lastname: Grimes
authors.forename: Burak
authors.initials: B
authors.lastname: Kutlu
authors.forename: Jan J
authors.initials: JJ
authors.lastname: Bot
authors.forename: David J
authors.initials: DJ
authors.lastname: Galas
mesh_terms: D002874:Chromosome Mapping; D019295:Computational Biology; D015894:Genome, Human; D005909:Glioblastoma / Q000235:genetics; D006801:Humans; D008957:Models, Genetic; D012984:Software