[ensembl-dev] Gene Symbol

[Andy Yates]

Hi Nick,

My guess is that you're hitting an issue with external synonyms. The method you are using will consult all xrefs linked to a gene (along with transcripts and translations) as well as consulting the external_synonym table. In the case of CLK2 we have the following external synonyms linked to the term CLK2.

synonym	db_name	dbprimary_acc	display_label
clk2	Vega_transcript	OTTHUMT00000364143	OTTHUMT00000364143
clk2	Vega_transcript	OTTHUMT00000365664	RP11-531A21.3-001
clk2	Vega_transcript	OTTHUMT00000272912	OTTHUMT00000272912
clk2	OTTG	OTTHUMG00000150164	OTTHUMG00000150164
CLK2	EntrezGene	9894	TELO2
clk2	HGNC	2069	CLK2

If you change your query to limit by the external DB of the source then the hits will reduce massively e.g.

my $genes = $gene_adaptor->fetch_all_by_external_name('CLK2', 'HGNC');

All the best

Andy

On 13 Feb 2012, at 15:22, Nick Fankhauser wrote:

> Hi!
> 
> I'm trying to retrieve the chromosomal position for a list of
> gene-symbols. They are all official gene-symbols.
> 
> Using a loop like this
> 
>    foreach my $gene
> (@{$gene_adaptor->fetch_all_by_external_name($gene_symbol)}) {
> 
> I get one correct hit for some genes (e.g. USP8), but for others like
> CLK2, I get multiple results and have no idea how to select the correct
> one. Is there a way to just get position of just the official gene symbol?
> 
> Thanks!
> 
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