How To Use Cytoscape To Do Gene Ontology Enrichment Analysis?

Question

[Jianguo Lu]

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.

[Vitis]

I think cytoscape is for visualizing networks, does it do GO term analysis?

Answer 1

[Russh]

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

[Yogesh Pandit]

Also take a look at the recently released plugin PiNGO http://www.psb.ugent.be/esb/PiNGO/Home.html. It requires BinGO to function

[Vitis]

blast2go to annotate (somewhat) your species first?

[Qdjm]

Are you involved in BinGO now? Do I have a feature wishlist for you!

[Russh]

nah, I've just used it and its ilk many many times

[Jianguo Lu]

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?

[User 8934]

Hi russH! do you need to built a network first to input into cytoscape to use BinGo?

Answer 2

[Madhan]

You can also try using ClueGO http://www.geneontology.org/GO.tools.microarray.shtml