[ensembl-dev] VEP distance cutoff

[Genomeo Dev]

Hi Nathan,

That is very interesting. How far are you with this method? Does it have a
name yet? For linking Genes to RegulatoryFeatures, what data this method is
based on?

G.


On 17 February 2014 13:08, njohnson <njohnson at ebi.ac.uk> wrote:

> Incidentally, our core software team is currently working on a method to
> associate any feature with a nearest gene.  In future this is likely to be
> used as part of a strategy to make Gene-RegulatoryFeature links.
>
> Nathan Johnson
>
> Ensembl Regulation
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
>
> http://www.ensembl.info/
> http://twitter.com/#!/ensembl
> https://www.facebook.com/Ensembl.org
>
> On 17 Feb 2014, at 12:36, Will McLaren <wm2 at ebi.ac.uk> wrote:
>
> > Yes, your assumption is correct - currently we do not carry any data
> linking regulatory features to specific genes, for exactly the reasons you
> state.
> >
> > Will
> >
> >
> > On 17 February 2014 12:31, Genomeo Dev <genomeodev at gmail.com> wrote:
> > Thanks.
> >
> > With regard to --regulatory option, Having run VEP with 1000G variants
> using this option I found that, in the output, whenever a variant is
> predicted to have a Feature type: RegulatoryFeature or MotifFeature, there
> is no entry in the GENE or SYMBOL columns and also unlike for variants with
> Feature type Transcript, CELL_TYPE is populated.
> >
> > Is this a reflection of the fact that current data in the Ensembl
> regulatory build are (1) cell-type specific (2) genome-wide profiling
> experiments which don't associate regulatory regions to the actual genes
> whose expression is being regulated?
> >
> > Thanks,
> >
> > G.
> >
> >
> >
> >
> >
> > On 17 February 2014 10:18, Will McLaren <wm2 at ebi.ac.uk> wrote:
> > Hello,
> >
> > The VEP looks at +/- 5KB either side of each transcript's start and end
> coordinates; these coordinates are inclusive of any UTR regions. A gene is
> defined by the furthest-reaching 5' and 3' coordinates of the transcripts
> in that gene. You might find the diagram on this page useful:
> >
> >
> http://www.ensembl.org/info/genome/variation/predicted_data.html#consequences
> >
> > The VEP separately annotates regulatory regions (in human and mouse at
> least) as determined by the Ensembl regulatory build; to enable this just
> add --regulatory to your VEP command.
> >
> > http://www.ensembl.org/info/genome/funcgen/regulatory_build.html
> >
> >
> http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_regulatory
> >
> > Regards
> >
> > Will McLaren
> > Ensembl Variation
> >
> >
> > On 17 February 2014 10:04, Genomeo Dev <genomeodev at gmail.com> wrote:
> > Hi,
> >
> > Thanks for the response. For a given variant, I assume VEP looks at the
> interval [-5KB, +5KB] and assigns as neighbours any genes which overlap
> with that region. How are genes defined in this case? Does VEP look only
> for overlapping TSS or the entire TSS<->TES region?
> >
> > How about variants which are documented in the literature to occur in
> enhancers which are say 1 MB from the target gene? Do these get taken into
> account on top of the 5KB rule?
> >
> > Thanks,
> >
> > G.
> >
> >
> >
> > On 5 February 2014 09:52, Genomeo Dev <genomeodev at gmail.com> wrote:
> > Thanks very much.
> >
> > G.
> >
> >
> > On 4 February 2014 22:02, Will McLaren <wm2 at ebi.ac.uk> wrote:
> > Hello,
> >
> > The default cutoff is 5000 bases.
> >
> > There is no parameter in the VEP itself, but there is a plugin available
> that can be used to change the parameter.
> >
> >
> https://github.com/ensembl-variation/VEP_plugins/blob/master/UpDownDistance.pm
> >
> > http://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html
> >
> > Regards
> >
> > Will McLaren
> > Ensembl Variation
> >
> >
> > On 4 February 2014 17:48, Genomeo Dev <genomeodev at gmail.com> wrote:
> > Hi,
> >
> > Using VEP in Ensembl VM v74
> >
> > 1. I was wondering what distance cutoff does VEP use to assign
> neighbouring genes to input variants.
> > 2. Is there a parameter to handle that?
> >
> > Thanks,
> >
> > Genomeo
> >
> >
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