[ensembl-dev] Gene Symbol
Andy Yates
ayates at ebi.ac.uk
Mon Feb 13 20:04:07 GMT 2012
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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