[ensembl-dev] Regulatory region variation

Graham Ritchie grsr at ebi.ac.uk
Mon May 16 12:03:24 BST 2011


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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