Document Type

Article

Publication Title

BMC Bioinformatics

Publisher

BioMed Central Ltd.

Publication Date

7-9-2013

Volume

14

Issue

217

Disciplines

Biology | Life Sciences

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 datahandling 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.

Keywords

Biological Networks, Visualization, Exploratory Data Analysis, Statistical Programming, Bioinformatics

DOI

10.1186/1471-2105-14-217

Rights

© 2013 Shannon et al.

Creative Commons License

Creative Commons Attribution 3.0 License
This work is licensed under a Creative Commons Attribution 3.0 License.

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Biology Commons

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