thank you very much,

for the gene ontology worked. I remeber there was something similar for Kegg
pathways. is there something similar now?

thank you



On Mon, Mar 16, 2009 at 4:52 PM, Marc Carlson <mcarlson@fhcrc.org> wrote:

> Hi John,
>
> Saroj is correct in that you should find the mappings you seek in the
> appropriate organism package ("org.Xx.eg.db" where "Xx" is the initial
> of the genus and species of the organism you are studying).  You
> probably want to look at the GO2ALLEGS mapping.
>
>  Marc
>
>
>
> Saroj K Mohapatra wrote:
> > Hi John:
> >
> > I do not have a general answer. However, the "org." packages do have a
> mapping from GO to Entrez gene. For example, there is the mouse package
> org.Mm.eg.db that has org.Mm.egGO which maps between the two identifiers.
> >
> >> library("org.Mm.eg.db")
> >> ?org.Mm.egGO2EG
> >>
> >
> > -----------
> >      org.Mm.egGO is an R object that provides mappings between entrez
> >      gene identifiers and the GO identifiers that they are  directly
> >      associated with. This mapping and its reverse mapping do NOT
> >      associate the child terms from the GO ontology with the gene.
> >      Only the directly evidenced terms are represented here.
> > -----------
> >
> > You could use the appropriate org package for your species.
> >
> > Hope this helps,
> >
> > Saroj
> >
> > ----- Original Message -----
> > From: "John Lande" <john.lande77@gmail.com>
> > To: bioconductor@stat.math.ethz.ch
> > Sent: Sunday, March 15, 2009 4:29:00 PM GMT -05:00 US/Canada Eastern
> > Subject: [BioC] GOLOCUSID
> >
> > dear Bioc,
> >
> > I have retrieved an old stript to extract genes associated with a
> specific
> > GO term from a previous release of BioC.
> >
> > it exploited the enviroment GOLOCUSID form the package GO.
> >
> > thei enviroment is no longer available in the current release bioc 2.3.
> > is there an equivalent enviroment in some other package?
> >
> > how can I retrieve the genes associated with a specific go term in bioc
> now.
> >
> > thank you
> >
> >       [[alternative HTML version deleted]]
> >
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> >
> >
>
>

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