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

O. Garcia (1) , Cosmin Saveanu (2) , M. Cline (1) , M. Fromont-Racine (2) , A. Jacquier (2) , B. Schwikowski (1) , T. Aittokallio (1)

1 Biologie systémique - Systems Biology
2 Génétique des Interactions Macromoléculaires

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

Keywords: User-Computer Interface; Software; Signal Transduction; Proteome; Biological; Models; Protein; Information Storage and Retrieval; Algorithms; Color; Computer Graphics; Computer Simulation; Databases

Domains: Life Sciences [q-bio]; Molecular Networks [q-bio.MN]

O. Garcia, Cosmin Saveanu, M. Cline, M. Fromont-Racine, A. Jacquier, et al.. GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring. Bioinformatics, 2007, 23 (3), pp.394 - 396. ⟨10.1093/bioinformatics/btl605⟩. ⟨pasteur-01404708⟩