How To Use Cytoscape To Do Gene Ontology Enrichment Analysis?
2
2
Entering edit mode
9.8 years ago
Jianguo Lu ▴ 200

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 cytoscape enrichment • 10k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
7
Entering edit mode
9.8 years ago
Russh ★ 1.2k

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 COMMENT
1
Entering edit mode

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 REPLY
1
Entering edit mode

blast2go to annotate (somewhat) your species first?

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode
9.6 years ago
Madhan ▴ 240

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

ADD COMMENT

Login before adding your answer.

Traffic: 2519 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6