<div dir="ltr">Thanks.<div><br></div><div>With regard to <font face="arial, sans-serif">--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 </font><span style="font-family:arial,sans-serif">Transcript</span><span style="font-family:arial,sans-serif">, CELL_TYPE is populated.</span></div>
<div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">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?</font></div>
<div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">Thanks,</font></div><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">G.</font></div><div><font face="arial, sans-serif"><br>
</font></div><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif"><br></font></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 17 February 2014 10:18, Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hello,<div><br></div><div>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:</div>
<div><br></div><div><a href="http://www.ensembl.org/info/genome/variation/predicted_data.html#consequences" target="_blank">http://www.ensembl.org/info/genome/variation/predicted_data.html#consequences</a><br></div><div>
<br></div><div>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.</div>
<div><br></div><div><a href="http://www.ensembl.org/info/genome/funcgen/regulatory_build.html" target="_blank">http://www.ensembl.org/info/genome/funcgen/regulatory_build.html</a><br></div><div><br></div><div><a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_regulatory" target="_blank">http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_regulatory</a><br>
</div><div class=""><div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><br><div class="gmail_quote">
On 17 February 2014 10:04, Genomeo Dev <span dir="ltr"><<a href="mailto:genomeodev@gmail.com" target="_blank">genomeodev@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi,<div><br></div><div>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?</div>
<div><br></div><div>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?</div><div><br></div><div>
Thanks,<br></div><div><br></div><div>G.<div><div><br><div class="gmail_extra"><br><br><div class="gmail_quote">On 5 February 2014 09:52, Genomeo Dev <span dir="ltr"><<a href="mailto:genomeodev@gmail.com" target="_blank">genomeodev@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Thanks very much.<span><font color="#888888"><div><br></div><div>G.</div></font></span></div>
<div><div><div class="gmail_extra"><br><br><div class="gmail_quote">On 4 February 2014 22:02, Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hello,<div><br></div><div>The default cutoff is 5000 bases.</div><div><br></div><div>There is no parameter in the VEP itself, but there is a plugin available that can be used to change the parameter.</div>
<div>
<br></div><div><a href="https://github.com/ensembl-variation/VEP_plugins/blob/master/UpDownDistance.pm" target="_blank">https://github.com/ensembl-variation/VEP_plugins/blob/master/UpDownDistance.pm</a><br></div><div><br>
</div><div><a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html" target="_blank">http://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html</a><br>
</div><div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><br><div class="gmail_quote"><div><div>On 4 February 2014 17:48, Genomeo Dev <span dir="ltr"><<a href="mailto:genomeodev@gmail.com" target="_blank">genomeodev@gmail.com</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div><div dir="ltr">Hi,<div><br></div><div>Using VEP in Ensembl VM v74</div><div><br></div>
<div>1. I was wondering what distance cutoff does VEP use to assign neighbouring genes to input variants.</div>
<div>2. Is there a parameter to handle that?</div>
<div><br></div><div>Thanks,</div><div><br></div><div>Genomeo</div><div><br></div></div>
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