[ensembl-dev] Regulatory region variation

[Agata Wesolowska]

Hi Graham,

Thanks for your fast answer. This approach however doesn't seem to work for
me.. I tried both with your given example of a SNP and some SNPs that were
annotated as "REGULATORY_REGION" in previous versions of Ensembl e.g.
rs13076120.

When I run the code I don't get any error messages, but I don't get any
annotation to regulatory regions either. I tried with all the 3 methods, but
in all cases the result was the same. Do you know what could be a possible
reason for that?

I have tried it both with a local installation of a database, and connecting
to your server. I also can't see a way to extract this information using
Biomart.

Best regards,

Agata

On Thu, May 12, 2011 at 5:07 PM, Graham Ritchie <grsr at ebi.ac.uk> wrote:
>
>> Hi Agata,
>>
>> We changed the consequence type calculation code for release 62 and the
>> way in which we integrate with the Regulation databases has changed
>> significantly. We used to only include consequences on regulatory regions
>> that were associated with transcripts somehow, but now you can find out if
>> your variants lie in any of the various types of feature stored in the
>> regulation database. There are 3 new methods in the VariationFeature class
>> that let you find out if your variant overlaps a feature from the regulation
>> database: get_all_RegulatoryFeatureVariations,
>> get_all_ExternalFeatureVariations and get_all_MotifFeatureVariations, the
>> objects returned from these methods have a similar interface as for
>> TranscriptVariations, so you can print out the consequence term with, for
>> example, the display_consequence method. Please refer to the API
>> documentation for more details, but here's a little bit of example code:
>>
>> my $vdba = $reg->get_DBAdaptor('human', 'variation');
>>
>> my $vfa = $vdba->get_VariationFeatureAdaptor;
>> my $va = $vdba->get_VariationAdaptor;
>>
>> my $v = $va->fetch_by_name('rs10054597');
>>
>> my $vf = $vfa->fetch_all_by_Variation($v)->[0];
>>
>> for my $rfv (@{ $vf->get_all_RegulatoryFeatureVariations }) {
>>    print $rfv->display_consequence, "\n";
>> }
>>
>> Regarding your second question, the regulation team store miRNA target
>> sites from miRanda in the regulation database as ExternalFeatures, so you
>> can check if your variant lies in one of these by calling
>> get_all_ExternalFeatureVariations and if any are returned checking if the
>> associated ExternalFeatureVariation->feature->feature_set->name is 'miRanda
>> miRNA targets'.
>>
>> Cheers,
>>
>> Graham
>>
>>
>> On 12 May 2011, at 15:02, Agata Wesolowska wrote:
>>
>> > Hi,
>> >
>> > I was extracting known SNPs together with their consequences on
>> transcripts from a list of genes using Ensembl API. I noticed that the
>> consequence "REGULATORY_REGION" is not present anymore among the possible
>> transcript consequences. Is there any reason for that? And is there any way
>> to obtain this information?
>> >
>> > Also another question - is it possible to find SNPs in microRNA target
>> sites using API?
>> >
>> > Best regards,
>> >
>> > Agata Wesolowska
>> >
>> >
>> >
>> >
>> > _______________________________________________
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>>
>>
>
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