[BioC] GO in Bioconductor

[Robert Gentleman]

Hi,
  For any chip, you can get it using the purpose built environments. For 
generic gene names, either biomaRt or some site such as NCBI can be 
used. But in general there are multiple GO ids for any gene (and you 
need to be a bit more careful in describing what you want - only the 
most specific GO terms or all GO terms - either are available in the 
meta-data packages, from other sources, you would need to get the most 
specific terms [generally that is what they give] and then build the GO 
graph. This can be done using tools in GOstats. The vignette there 
should be self-explanatory, if not please let me know (on this list) 
what problems you encounter,

  best wishes
   Robert


Kaustubh Patil wrote:
> Dear John,
>  
>  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?
>  
>  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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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org