[ensembl-dev] Ensembl Gene ID of Motif Feature
ilavidas at ebi.ac.uk
Thu Apr 30 18:58:52 BST 2020
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
As a result the reported match score can be quite varied among motif
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
> Best regards
> 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,
>>> 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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> Souhila Amanzougarene
> Dev mailing list Dev at ensembl.org
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