However, the increasing number and redundancy of -gene-sets used by many current enrichment analysis resources work against this ideal. Ideally, the number of resulting sets is smaller than the number of genes in the list, thus simplifying interpretation. Gene-set enrichment analysis finds functionally coherent gene-sets, such as pathways, that are statistically overrepresented in a given gene list. (2011) Visualizing gene-set enrichment results using the Cytoscape plug-in enrichment map. AVAILABILITY AND IMPLEMENTATION: The GeneMANIA Cytoscape plugin is implemented in Java and is freely available at. Users may add their own interaction networks and expression profile data to complement or override the default data. The plugin uses over 800 networks from six organisms and each related gene is traceable to the source network used to make the prediction. GeneMANIA identifies the most related genes to a query gene set using a guilt-by-association approach. UNLABELLED: The GeneMANIA Cytoscape plugin brings fast gene function prediction capabilities to the desktop. (2010) GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop.
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