[BioC] GO in Bioconductor

[John Zhang]

> Thank you very much for your reply. I would like to know, how to get GOID from 
gene name? Is it possible using BioC or I have to do it explicitely?

I would get it from NCBI.

> 
> Regards,
> Kaustubh
>
>John Zhang <jzhang at jimmy.harvard.edu> wrote: 
>> How can I use Gene Ontology in BioC? Is there any tutorial or manual 
>available? Especially how can I construct (extract) a tree if I have a gene 
name 
>(e.g. RAD52)
>
>GO() lists all the environments of the GO package.
>?environment name gives you the description of the environment of interest with 
>some example code.
>
>For the thing you would like to do you may try to get the Gene id for the gene 
>(e. g. 19365) and then do the following:
>
>> goids <- get("19365", GOLOCUSID2GO)
>
>You will get a few goids the gene maps to. Suppose we are interested in 
>GO:0005515 that belongs to MF.
>
>> get("GO:0005515", GOMFPARENTS) # Get the direct parents 
>> get("GO:0005515", GOMFCHILDREN) # Get the direct children
>> get("GO:0005515", GOMFANCESTOR) # Get the parents and grand parents ...
>> get("GO:0005515", GOMFOFFSPRING) # Get the children and grand children ...
>
>The above do not give you enough to construct a GO tree but you can always 
>search the Gene Ontology web site for a tree.
>
>
>
>> 
>> Thanks and regards,
>> Kaustubh
>> 
>>
>>  
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>
>Jianhua Zhang
>Department of Medical Oncology
>Dana-Farber Cancer Institute
>44 Binney Street
>Boston, MA 02115-6084
>
>
>
>
>			
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> Ring in the New Year with Photo Calendars. Add photos, events, holidays, 
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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084