How to use cytoscape to do the gene ontology enrichment analysis? And how to use cytoscape to classify 3 different categories, biological process, cellular component, and molecular function for all the genes.
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Jianguo Lu
2 answers
Cytoscape can very definitely be used for GO term analysis and can do many things beyond network visualisation.
Have a look at BinGO in the plugin list here. The user guide at the BinGO website here should help you do what you need.
Could you tell us which species you are working with? Regards, Russ
I am working on fish species. But except zebrafish, other fish species do not have too much GO information. BinGO also works for these species?
Also take a look at the recently released plugin PiNGO http://www.psb.ugent.be/esb/PiNGO/Home.html. It requires BinGO to function
Hi russH! do you need to built a network first to input into cytoscape to use BinGo?
You can also try using ClueGO http://www.geneontology.org/GO.tools.microarray.shtml
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I think cytoscape is for visualizing networks, does it do GO term analysis?