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

[Giovanni Marco Dall'Olio]

On Fri, Jan 8, 2010 at 11:47 AM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> Please CC the mailing list in replies.
>
> On Fri, Jan 8, 2010 at 10:20 AM, Sameet Mehta <msameet at gmail.com> wrote:
>> Hi,
>> Thanks for the reply.  What I have are the old GeneSymbols.  I have
>> already selected the genes of interest based on expression profiles.
>> But I need their current GeneSymbols, so that I can do GO-Term
>> enrichment.


I would do it with BioMart, as it already has all the datasets
available and it makes it possible to do it without programming at
all. I know you can do it with biopython, but this is just a one-time
job, maybe it is not necessary...

In any case, it is true that you can't do it without knowing which
GeneSymbols you are using and with which version they were annotated.


>
> Yes, but which GeneSymbols do you have? There are lots of
> different ones (including different species - for human you would
> probably be talking about the HUGO Gene Nomenclature
> Committee assigned symbols).
>
> Assuming your particular gene symbols are covered, then using
> NCBI Entrez and the Gene database might work (try ELink?).
>
> Peter
>
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-- 
Giovanni Dall'Olio, phd student
Department of Biologia Evolutiva at CEXS-UPF (Barcelona, Spain)

My blog on bioinformatics: http://bioinfoblog.it