[ensembl-dev] Regulatory region variation

[Agata Wesolowska]

Hi again,

I run the script you sent and I still don't see any output.

Best,

Agata

On Mon, May 16, 2011 at 12:26 PM, Graham Ritchie <grsr at ebi.ac.uk> wrote:

> Hi Agata,
>
> If I try your example variant (rs13076120) in the script I sent you I get a
> REGULATORY_REGION consequence on ENSR00001374087. Can you run the code below
> and let me know if you don't see any output?
>
> These consequences are calculated on the fly by the API and aren't stored
> in the database so they're not available in biomart at the moment. We may
> rethink this though if there is a requirement for these consequences to be
> available in the variation mart.
>
> Cheers,
>
> Graham
>
> -----
>
> use Bio::EnsEMBL::Registry;
>
> my $reg = 'Bio::EnsEMBL::Registry';
>
> $reg->load_registry_from_db(
>    -host   => 'ensembldb.ensembl.org',
>    -user   => 'anonymous',
> );
>
> my $vdba = $reg->get_DBAdaptor('human', 'variation');
> my $vfa = $vdba->get_VariationFeatureAdaptor;
> my $va = $vdba->get_VariationAdaptor;
>
> my $v = $va->fetch_by_name('rs13076120');
> my $vf = $vfa->fetch_all_by_Variation($v)->[0];
>
> for my $rfv (@{ $vf->get_all_RegulatoryFeatureVariations }) {
>     print $rfv->feature->stable_id, ": ", $rfv->display_consequence, "\n";
> }
>
>
> On 16 May 2011, at 10:35, Agata Wesolowska wrote:
>
> > 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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>
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