[ensembl-dev] Regulatory region variation

[Graham Ritchie]

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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