Question: How To Use Cytoscape To Do Gene Ontology Enrichment Analysis?
2
gravatar for Jianguo Lu
8.3 years ago by
Jianguo Lu200
Auburn, AL
Jianguo Lu200 wrote:

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.

gene enrichment cytoscape • 8.5k views
ADD COMMENTlink written 8.3 years ago by Jianguo Lu200

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

ADD REPLYlink written 8.3 years ago by Vitis2.3k
7
gravatar for Russh
8.3 years ago by
Russh1.2k
U. Liverpool
Russh1.2k wrote:

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

ADD COMMENTlink written 8.3 years ago by Russh1.2k
1

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

ADD REPLYlink written 8.3 years ago by Yogesh Pandit500
1

blast2go to annotate (somewhat) your species first?

ADD REPLYlink written 8.3 years ago by Vitis2.3k

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

ADD REPLYlink written 8.3 years ago by Qdjm1.9k

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

ADD REPLYlink written 8.3 years ago by Russh1.2k

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?

ADD REPLYlink written 8.3 years ago by Jianguo Lu200

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

ADD REPLYlink written 8.0 years ago by User 893450
0
gravatar for Madhan
8.0 years ago by
Madhan220
United States
Madhan220 wrote:

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

ADD COMMENTlink written 8.0 years ago by Madhan220
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