[Biopython] how to obtain official Gene Symbols for a list of GeneNames

[Peter Cock]

On Fri, Jan 8, 2010 at 7:09 AM, Sameet Mehta <msameet at gmail.com> wrote:
> Hi All,
>
> I have a few lists of gene names/gene symbols for some old (5 year
> old) microarray experiments.  I want to find out the official Gene
> Symbols for all of these genes.  Is there a way to do it in Biopython.
>
> regards
> Sameet

I'd start by working out whose gene names/gene symbols they are.
What kind of microarrays are you using? For a custom chip you may
have to talk to whomever designed it, but for mainstream commercial
chips there should be lookup tables, either on the manufacturors
website or perhaps in R/Bioconductor.

Note you can actually combine R/Bioconductor with Python using
rpy2 (or its predecessor, rpy). For examples, see:

http://bcbio.wordpress.com/2010/01/02/automated-retrieval-of-expression-data-with-python-and-r/
http://www.warwick.ac.uk/go/peter_cock/python/heatmap/

Peter