mcarlson at fhcrc.org
Tue Mar 24 19:15:27 CET 2009
Because the KEGG pathway IDs have a species specific ID in front of
them, those can still be found in KEGG.db. Look for the
KEGGPATHID2EXTID and KEGGEXTID2PATHID mappings.
John Lande wrote:
> 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 at fhcrc.org
> <mailto:mcarlson at 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.
> 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
> > 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 at gmail.com
> <mailto:john.lande77 at gmail.com>>
> > To: bioconductor at stat.math.ethz.ch
> <mailto:bioconductor at 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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