[ensembl-dev] Gene Symbol

[Nick Fankhauser]

Hi!

yes, you're right, it works! I just realized that many of my
gene-symbols were not actually the official ones, but aliases. So I
guess I have to translate those by hand, then it should work like this.

Or how could I get the display_label from the gene-adaptor, then it
would also be possible using the other method, maybe?

Yours,
Nick

On 13/02/12 21:04, Andy Yates wrote:
> Hi Nick,
> 
> Apologies that method had slipped my mind & you are right you can use fetch_by_display_label() instead.
> 
> Andy
> 
> Andrew Yates                   Ensembl Core Software Project Leader
> EMBL-EBI                       Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK         http://www.ensembl.org/
> 
> On 13 Feb 2012, at 19:56, Nick Fankhauser wrote:
> 
>> Hi!
>>
>> Thanks!
>> But how can I get the display_label from a gene adaptor?
>>
>> And couldn't I just have used fetch_by_display_label instead of
>> fetch_all_by_external_name in the first place to retrieve the gene by
>> gene-symbol?
>>
>> Yours,
>> Nick
>>
>> On 13/02/12 18:05, Andy Yates wrote:
>>> Hi Nick,
>>>
>>> Again it's an issue with synonyms. If we take the case of SF3B1 we get two hits back:
>>>
>>> http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000115524;r=2:198256698-198299815
>>>
>>> http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000087365;r=11:65818200-65836779;t=ENST00000528302
>>>
>>> The first is the intended record. The second is SF3B2 but this has a synonym for SF3b1 which is returned because our MySQL tables are case insensitive. If you add a check on the display label that should remove the remaining stragglers.
>>>
>>> Andy
>>>
>>> Andrew Yates                   Ensembl Core Software Project Leader
>>> EMBL-EBI                       Tel: +44-(0)1223-492538
>>> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
>>> Cambridge CB10 1SD, UK         http://www.ensembl.org/
>>>
>>> On 13 Feb 2012, at 16:26, Nick Fankhauser wrote:
>>>
>>>> Yes, thanks a lot! Like this it produces a lot less false hits.
>>>> Especially when I combine it with rejecting all MHC chromosomes.
>>>>
>>>> But there's still for example SF3B1 and RAGE, for which I get results
>>>> from two different chromosomes for some reason. Do you know why this can
>>>> still be the case?
>>>>
>>>> Nick
>>>>
>>>>
>>>> On 13/02/12 17:00, Andy Yates wrote:
>>>>> 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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>>>>>
>>>>>
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>