Affiliations: The Hamner Institutes for Health Sciences, 6 Davis
Drive, Research Triangle Park, NC 27709-2137, USA | Genomics Institute of the Novartis Research
Foundation, 10675 John J. Hopkins Drive, San Diego, CA 92121, USA | Institute for Translational Medicine and Therapeutics,
810 Biomedical Research Building, University of Pennsylvania School of
Medicine, 421 Curie Boulevard, Philadelphia, PA 19104-6160, USA
Note: [] Corresponding author. The Hamner Institutes for Health Sciences,
6 Davis Drive, PO Box 12137, Research Triangle Park, NC 27709-2137, USA.
E-mail: [email protected]
Abstract: Graphical methods are useful for visualizing signaling networks
derived from the synthesis of large bodies of literature information or
large-scale experimental measurements. Software tools to filter and organize
these networks allow the exploration of their inherent biological and
structural properties. We have developed NetAtlas, an open-source, Java-based
Cytoscape plugin for examining signaling networks in the context of tissue gene
expression patterns. The tissue gene expression data available through NetAtlas
consists of 79 human tissues, 61 mouse tissues, and 44 combined tissues from 3
rat strains. Users may also import their own tissue gene expression data. The
NetAtlas plugin allows the creation of tissue-defined signaling networks by
identifying which components are expressed in particular tissues, which
components show tissue-specific expression, and which components within the
network are coordinately expressed across tissues. The NetAtlas plugin is
available at http://sourceforge.net/projects/netatlas/.
