[BioC] GO in Bioconductor

[Ting-Yuan Liu]

Hi Kaustubh,

If you are using specific gene chips that BioC builds the annotation 
package for them, you can do the following instead of going to NCBI 
website.  

For example, if you are using Affymetrix Human Genome U95 Set Gene Chip, 
the annotation package hgu95av2 is designed for it.  

Suppose that you are interested in the GOID of the following gene names:
"tubulin, beta 3", "POU domain, class 2, transcription factor 2", and "BTG 
family, member 2".  Then first you have to figure out which probe set ids 
in this chip are associated with these three gene names.  Do the 
following:

library(hgu95av2)
geneName <- c("tubulin, beta 3", "POU domain, class 2, transcription 
factor 2", "BTG family, member 2")
geneNameAll <- unlist(as.list(hgu95av2GENENAME))
geneIndex <- match(geneName, geneNameAll)
probeSetIds <-names(geneNameAll[geneIndex])

Then the next step is to find out the GOIDs for these probeSetIds by using 
hgu95av2GO:

mget(probeSetIds, hgu95av2GO)


If you are not using specific gene chip with annotation package 
available, you have to get the GOIDs from NCBI website as John suggested.

HTH,
Ting-Yuan
______________________________________
Ting-Yuan Liu
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
Seattle, WA, USA
______________________________________

On Thu, 5 Jan 2006, John Zhang wrote:

> 
> > 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
> >
> >
> >
> >
> >			
> >---------------------------------
> >Yahoo! Photos
> > Ring in the New Year with Photo Calendars. Add photos, events, holidays, 
> whatever.
> Jianhua Zhang
> Department of Medical Oncology
> Dana-Farber Cancer Institute
> 44 Binney Street
> Boston, MA 02115-6084
> 
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