[BioC] retrieve the gene symbols, full names etc given list of Entrez Gene IDs

James W. MacDonald jmacdon at med.umich.edu
Sun Jul 2 02:14:41 CEST 2006

Luo Weijun wrote:
> Hello all,
> Is there anyway to retrieve the gene symbols, full
> names (discription), or other gene information, given
> a list of Entrez Gene IDs (or the LocusLink) in
> Bioconductor. Obviously, one way is to query Entrez
> Gene web service ID by ID, but is there any way to get
> connected to that web service from within
> R/Bioconductor and retrieve the specific fields only(
> like gene symbol, Name, Chromosome, MIM etc) of Entrez
> Gene Records?
> biomaRt seems to require interactive R, and mine is
> command-line, 

I don't know what interactive R might be, and how that might differ from 
command line. As far as I know, there is only one 'type' of R (pretty 
much command line, unless you are using some tcl/tk widgets), and 
biomaRt works for that.

and also it doesn't make one-on-one
> mapping table since multiple ensemble IDs map to one
> Entrez Gene ID, which is very annoying in making a
> good-looking annotation table.

Again, not sure what you are getting at here. There are many things in 
the annotation world that don't have a neat one-to-one mapping. Anyway, 
have you looked at the vignette in biomaRt that shows how to make an 
annotated HTML table using biomaRt and annotate? This cleanly handles 
any one-to-many annotations, and the result isn't completely horrible to 
look at...



> Thank you so much.
> Weijun
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James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109

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