RCytoscape: Tools for exploratory network analysis

Paul T. Shannon, Mark Grimes, Burak Kutlu, Jan J. Bot, David J. Galas

Research output: Contribution to journalArticlepeer-review

81 Scopus citations

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.

Original languageEnglish
Article number217
JournalBMC Bioinformatics
Volume14
Issue number1
DOIs
StatePublished - Jul 9 2013

Keywords

  • Bioinformatics
  • Biological networks
  • Exploratory data analysis
  • Statistical programming
  • Visualization

Fingerprint

Dive into the research topics of 'RCytoscape: Tools for exploratory network analysis'. Together they form a unique fingerprint.

Cite this