Tools for GO term enrichment in prokaryotes
1
2
Entering edit mode
ksw ▴ 20
@ksw-8559
Last seen 7.3 years ago
United States

Hi,

I am new to gene ontology and was wondering the best tool to use to test if a gene set is enriched for certain GO terms in a non-model prokaryote?

 

Thank you!

bacteria GO enrichment • 1.6k views
ADD COMMENT
1
Entering edit mode
Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 6.3 years ago
United States

Hi,

So the tricky part here is that you are looking at a non-model prokayote and you need GO to gene mappings to do the kind of analysis that you propose.  Where could you find these?  Well that depends on just how 'non-model' your organism is...  If your organism doesn't have assigned gene IDs and associated GO terms, then you are going to have to do some extra work up front in order to infer them somehow.


But if your organism has gene IDs, then there are several possible.  One is to use the mappings from UniProt.   You can often get this kind of information by using the UniProt.ws package if your organism has a valid taxonomy id.   Here is an example of what that would look like

library(UniProt.ws)
up <- UniProt.ws(511145)
res <- select(up, keys(up,'UNIPROTKB'), 'GO-ID', 'UNIPROTKB')

 

Hope that helps,

 

Marc

ADD COMMENT

Login before adding your answer.

Traffic: 386 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