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Bioinformatics Advance Access originally published online on November 24, 2006
Bioinformatics 2007 23(3):394-396; doi:10.1093/bioinformatics/btl605
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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

Olivier Garcia 1, Cosmin Saveanu 2, Melissa Cline 1, Micheline Fromont-Racine 2, Alain Jacquier 2, Benno Schwikowski 1 and Tero Aittokallio 1,*

1 Systems Biology Unit, Institut Pasteur 75724 Paris Cedex 15, France
2 Macromolecular Interaction Genetics, Institut Pasteur 75724 Paris Cedex 15, France

*To whom correspondence should be addressed.


  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 highlights 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

Contact: teanai{at}pasteur.fr

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

Associate Editor: Alvis Brazma

Received on October 18, 2006; revised on November 21, 2006; accepted on November 21, 2006

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K. Kojima, M. Nagasaki, and S. Miyano
Fast grid layout algorithm for biological networks with sweep calculation
Bioinformatics, June 15, 2008; 24(12): 1433 - 1441.
[Abstract] [Full Text] [PDF]


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