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. 2011 Apr 1;27(7):1030-1.
doi: 10.1093/bioinformatics/btr045. Epub 2011 Jan 28.

PiNGO: a Cytoscape plugin to find candidate genes in biological networks

Michael Smoot  1 , Keiichiro Ono, Trey Ideker, Steven Maere
Affiliations

PiNGO: a Cytoscape plugin to find candidate genes in biological networks

Michael Smoot et al. Bioinformatics. .

Abstract

PiNGO is a tool to screen biological networks for candidate genes, i.e. genes predicted to be involved in a biological process of interest. The user can narrow the search to genes with particular known functions or exclude genes belonging to particular functional classes. PiNGO provides support for a wide range of organisms and Gene Ontology classification schemes, and it can easily be customized for other organisms and functional classifications. PiNGO is implemented as a plugin for Cytoscape, a popular network visualization platform.

Availability: PiNGO is distributed as an open-source Java package under the GNU General Public License (http://www.gnu.org/), and can be downloaded via the Cytoscape plugin manager. A detailed user guide and tutorial are available on the PiNGO website (http://www.psb.ugent.be/esb/PiNGO.

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Figures

Fig. 1.
Fig. 1.
A sample PiNGO analysis on an ENIGMA (Maere et al., 2008) co-differential expression network learned from the budding yeast microarray compendium of Hughes et al., (2000). ‘Conjugation’ (GO:0000746) was specified as the only filter and target GO category, and ‘transcription regulator activity’ (GO:0030528) as the start GO category. Darker nodes are more significantly associated with (a subcategory of) conjugation. White nodes are known conjugation genes. The area of a colored node is proportional to the number of neighboring conjugation genes.
See this image and copyright information in PMC

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