[BioC] Getting GO term from GOids

[James W. MacDonald]

Hi Alex,

Alex Tsoi wrote:
> Thanks for the information, but I guess GOHyperG does not output the Gene
> ontology term, while hyperGTest output both the GOid, as well as the  GO
> term. However, my another question is how could I retrieve information about
> the genes that have the enriched gene ontology (ie. which genes are
> annotated with the enriched gene ontology)?
>   

There is a function in affycoretools (hyperGoutput()) that does pretty 
much what I think you want to do.

Best,

Jim


> The hyperGTest gives us information about the count of the differentially
> expressed genes that are annotated with that enriched gene ontology, and it
> also gives the count of the genes in the array that are annotated with the
> GO, but I would like to have information about which differentially
> expressed genes are annotated with those GO. So I guess my question is given
> a set of Locus link ID, is it possible to find the gene ontologies
> associated with them by using the array's package : hgu133plus2 ?
>
> (I tried to use GOLOCUSID2GO to find all the ontologies associated with each
> of the differentially expressed genes, and see if each of the ontology is
> enriched by looking back the result of the hyperGTest,  but I found the
> results are not coherent; ie. the GO annotations of the package hgu133plus2
> is not coherent with the result of the GOLOCUSID2GO )
>
> So that's why I would like to retrieve the GO ids from a set of locus link
> ids.
>
> Appreciate for any help or comment
>
>
>
> On 7/23/07, Seth Falcon <sfalcon at fhcrc.org> wrote:
>   
>> "Alex Tsoi" <tsoi.teen at gmail.com> writes:
>>
>>     
>>> Dear all,
>>>
>>> I am using GOHyperG to get the onverrepresented gene ontology of a set
>>>       
>> of
>>     
>>> genes, and the results give the gene ontology IDs, I just wondering if I
>>> could also get the gene ontology terms in the results ;
>>>       
>> What do you mean by terms?  Does the summary method on the test result
>> do what you want?  Try:
>>
>>     ans <- hyperGTest(yourParams)
>>     summary(ans)
>>
>>     
>>> and also, could someone shows me how I could get the gene ontology
>>> terms from a set of gene ontology IDs ?
>>>       
>> Perhaps you want:
>>
>>    library("GO")
>>    someGOTerms <- mget(someGOIDs, GOTERM)
>>
>> Have you had a look at the vignette that comes with GOstats?  Try:
>>
>>    library("GOstats")
>>    openVignette(package="GOstats")
>>
>>
>> + seth
>>
>> --
>> Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research
>> Center
>> http://bioconductor.org
>>
>>     
>
>
>
>   


-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623