GOlorize

GOlorize provides class-guided network visualization in Cytoscape. GOlorize uses Gene Ontology (GO) categories or other additional class information to direct the network graph layout process and to emphasize the biological function of the nodes. It can be used in conjunction with the BiNGO plug-in, an efficient tool to find the GO categories that are overrepresented in a selected part of the network. GOlorize first highlights the nodes that belong to the same class using color-coding and then constructs an enhanced visualization of the network using a class-directed layout algorithm. Citation: Garcia O, Saveanu C, Cline M, Fromont-Racine M, Jacquier A, Schwikowski B, and Aittokallio T. GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring. Bioinformatics 2007, 23(3): 394-6.

___GOlorize for Cytoscape version 2.4.x and BiNGO version 2.x___

Release date: Feb. 12, 2007

Major new features

  • Incorporates the new BiNGO code, version 2.0
  • Allows also attribute-based node class definitions
  • Easy-to-use slider to adjust rendering properties
Downloads

___GOlorize for Cytoscape version 2.2.x and BiNGO version 1.x___

Release Date: Oct. 17, 2006

Downloads

___Acknowledgements___

Thanks to Steven Maere for his great help in incorporating BiNGO in GOlorize, and the Cytoscape developer team, especially Mike Smoot, for making GOlorize compatible with the Cytoscape, version 2.4. The research was partly funded by NIH Grant 1 R01 GM070743.

This plug-in and Cytoscape software are made available under the GNU Public License, which means that the source code is freely available for use within other software, but if you alter the code itself and distribute it, you must make the new source code freely available as well.