[ensembl-dev] VEP distance cutoff

[njohnson]

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

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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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