[ensembl-dev] Regulatory region variation

Agata Wesolowska agata at cbs.dtu.dk
Mon May 16 12:58:06 BST 2011


Hi Graham,

Thanks again, it turns out I didn't have the regulation API installed. Now
it works as it's supposed to.

Best,

Agata

On Mon, May 16, 2011 at 1:03 PM, Graham Ritchie <grsr at ebi.ac.uk> wrote:

> Hi Agata,
>
> Are you running the version 62 API and connecting to release 62 databases?
> You will also need the regulation API installed if you don't already have it
> - there are some instructions on how to get it here:
>
> http://www.ensembl.org/info/docs/api/api_installation.html
>
> Note that (for historical reasons) the regulation repository is called
> ensembl-functgenomics
>
> Cheers,
>
> Graham
>
>
> On 16 May 2011, at 11:47, Agata Wesolowska wrote:
>
> > 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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