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Bioinformatics Advance Access published online on November 24, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl605
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© 2006 The Author(s)
Received October 18, 2006
Accepted November 21, 2006

Applications note

GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring

Olivier Garcia 1, Cosmin Saveanu 1, Melissa Cline 1, Micheline Fromont-Racine 1, Alain Jacquier 1, Benno Schwikowski 1, and Tero Aittokallio 1 *

1 Institut Pasteur, FR-75724 Paris Cedex 15, France

* To whom correspondence should be addressed.
Tero Aittokallio, E-mail: teanai{at}pasteur.fr


  Abstract

Summary: We have implemented a graph layout algorithm that exposes Gene Ontology (GO) class structure on the network nodes. It can be used in conjunction with BiNGO plug-in to Cytoscape, which finds the GO categories over-represented in a given network. Our plug-in, named GOlorize, first high-lights the class members with category-specific color-coding and then constructs an enhanced visualization of the network using a class-directed layout algorithm.

Availability: http://www.cytoscape.org/plugins2.php.

Supplementary information: Installation instructions and tutorial at http://www.cytoscape.org/plugins/GOlorize/GOlorizeUserGuide.pdf.

Associate Editor: Alvis Brazma
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Fast grid layout algorithm for biological networks with sweep calculation
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[Abstract] [Full Text] [PDF]


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