[ensembl-dev] VEP distance cutoff

[Will McLaren]

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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>>>>>
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>>>
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>>
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>
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