[ensembl-dev] Ensembl Gene ID of Motif Feature

[Ilias Lavidas]

Dear Souhila,
Defining a specific cutoff score is not very easy, as this is something 
that varies across cell types.
Since we are focused on potential binding within our predicted 
regulatory elements, we set a non strict p-value in the detection 
algorithm that we used so that we wouldn't miss potentially interesting 
sites.
As a result the reported match score can be quite varied among motif 
features.

Kind Regards,
Ilias




On 30/04/2020 18:00, Souhila Amanzougarene wrote:
>
> Hi Anja,
>
> Thanks a lot for your response.
>
> I understand. Yes, I wanted to get taget gene that is regulated by a 
> given motif feature.
>
> I have another question about the *motif score change,* I don't 
> understand when can we say that the difference in motif scoreis high 
> or low, is there a threshold ? How to interpret the negatif or positif 
> diffeneces?
>
>
> Best regards
>
>
> Souhila
>
> *
> *
>
> Le 29/04/2020 à 13:47, Anja Thormann a écrit :
>> Dear Souhila,
>>
>> we don’t have any information about the gene that is regulated by a 
>> given motif feature if that is what you were after. Please let me 
>> know if that is not the case. VEP returns gene IDs for variants which 
>> overlap transcripts.
>>
>> Best regards,
>> Anja
>>
>>
>>> On 27 Apr 2020, at 16:35, Souhila Amanzougarene 
>>> <souhila.amanzougarene at cnrs.fr 
>>> <mailto:souhila.amanzougarene at cnrs.fr>> wrote:
>>>
>>> Hi Ensembl Developers,
>>>
>>> I used VEP to annotate vcf files, I'm interested by the 
>>> *MotifFeature*. In the annotated file, I have only the ensembl motif 
>>> ID (Feature column).
>>>
>>> Is there any way to get gene ID in addition of the ensembl motif ID.
>>>
>>> Best regards
>>>
>>> -- 
>>> Souhila Amanzougarene
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>>
>>
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> -- 
> Souhila Amanzougarene
>
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