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Question: Tools for GO term enrichment in prokaryotes
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gravatar for ksw
2.3 years ago by
ksw20
United States
ksw20 wrote:

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!

ADD COMMENTlink modified 2.3 years ago by Marc Carlson7.2k • written 2.3 years ago by ksw20
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gravatar for Marc Carlson
2.3 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:

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 COMMENTlink written 2.3 years ago by Marc Carlson7.2k
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