[BioC] how to get gene list for given GO terms?

[Ou, Jianhong]

Hi Martin,

Thank you for your reply. 

The question may be divided into two parts. The first part is like what you replied. The second one is that maybe the given GO term is the ancestor of other GO terms which are not annotated in the org.Hs.egGO db.

I what I did for this is that fist map all the gene entrez_id into GO terms and get all the ancestor of the GO terms. Then go back to extract all the genes involved in one GO term.

I will appreciated if there is any package can do this.

Yours sincerely,

Jianhong Ou

jianhong.ou at umassmed.edu


On Feb 29, 2012, at 1:47 PM, Martin Morgan wrote:

> On 02/27/2012 04:41 PM, Ou, Jianhong wrote:
>> Hello All,
>> 
>> Is there any package can extract a gene list for a given GO term from human genome?
> 
> 
> For instance
> 
> library(org.Hs.egGO)
> revmap(org.Hs.egGO)[["GO:0042254"]]
>     IEA      IEA      IEA      IEA      IEA      IBA      IEA      IEA
>   "705"   "3692"   "4809"   "6130"   "6175"   "6222"   "6838"  "10171"
>     IEA      IEA       IC      NAS      IEA      IEA      IEA      IEA
> "10969"  "23212"  "23246"  "23246"  "23560"  "26164"  "26284"  "26574"
>     IEA      IEA      IEA      IEA      IEA      IEA      IEA      IEA
> "29102"  "29889"  "51154"  "51187"  "54552"  "54680"  "55299"  "79631"
>     IEA      IEA      IEA      IDA      IEA
> "81875"  "84864"  "85865"  "92345" "124995"
> 
> see
> 
>  vignette(package="AnnotationDbi", "AnnotationDbi")
> 
> Martin
> 
>> 
>> Thanks a lot.
>> 
>> Yours sincerely,
>> 
>> Jianhong Ou
>> 
>> jianhong.ou at umassmed.edu
>> 
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> 
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