Abstract

- Communication -

NetAtlas: A Cytoscape plugin to examine signaling networks based on tissue gene expression

Longlong Yang¹, John R. Walker², John B. Hogenesch³ and Russell S. Thomas¹*

¹ The Hamner Institutes for Health Sciences, 6 Davis Drive, Research Triangle Park, NC 27709-2137, USA
² Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Drive, San Diego, CA 92121, USA
³ Institute for Translational Medicine and Therapeutics, 810 Biomedical Research Building, University of Pennsylvania School of Medicine, 421 Curie Boulevard, Philadelphia, PA 19104-6160, USA

* Corresponding authors
The Hamner Institutes for Health Sciences, 6 Davis Drive, PO Box 12137, Research Triangle Park, NC 27709-2137, USA
Email: rthomas@thehamner.org

Edited by H. Michael; received August 02, 2007; revised November 20, 2007; accepted November 21, 2007; published December 06, 2007

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 plug is available at http://sourceforge.net/projects/netatlas/

Keywords: tissue gene expression, signaling networks, pathway visualization