[ensembl-dev] Motif feature consequences discrepancy

[Anja Thormann]

Hi Sigurjón,

unfortunately there is no straightforward way of getting overlaps with unverified motif features. We are providing GFF dumps with all motif features here ftp://ftp.ensembl.org/pub/release-99/regulation/homo_sapiens/MotifFeatures/ <ftp://ftp.ensembl.org/pub/release-99/regulation/homo_sapiens/MotifFeatures/>.

VEP does support custom annotation. However, at the moment VEP still lacks the option to create features similar to transcripts from a GFF file containing motif features. We are working on it and hopefully should support this use case in a coming release.

If you have a chance to convert the GFF files into BED files you can use VEP’s custom annotation option for BED files: https://www.ensembl.org/info/docs/tools/vep/script/vep_custom.html <https://www.ensembl.org/info/docs/tools/vep/script/vep_custom.html>

We also display all motif features in our browser: https://jan2020.archive.ensembl.org/Homo_sapiens/Share/0b737ea4a480564bb963aa2f4a019461?redirect=no;mobileredirect=no <https://jan2020.archive.ensembl.org/Homo_sapiens/Share/0b737ea4a480564bb963aa2f4a019461?redirect=no;mobileredirect=no> which could be useful if you want to look up individual cases.	


Best wishes,
Anja


> On 12 Mar 2020, at 13:55, Sigurjón Axel Guðjónsson <Sigurjon.Gudjonsson at decode.is> wrote:
> 
> Hi Anja,
>  
> Thank you for explaining this.
>  
> Would it be possible to optionally show unverified motif features in VEP.  I.e. if the relevant cell line is missing ChIP-Seq peak data.
>  
> Best regards,
> Sigurjón
>  
>  
> From: Dev <dev-bounces at ensembl.org> On Behalf Of Anja Thormann
> Sent: fimmtudagur, 12. mars 2020 13:12
> To: Ensembl developers list <dev at ensembl.org>
> Subject: Re: [ensembl-dev] Motif feature consequences discrepancy
>  
> Hi Sigurjon,
>  
> VEP only reports overlaps with 'experimentally verified’ motif features. Which means those motif features fully overlap with a relevant ChIP-Seq peak. On the website we are still showing overlaps with unverified motif features. This will be updated for next release 100 when we are only going to show overlaps with 'experimentally verified’ motif features. Our blog post <http://www.ensembl.info/2018/10/15/new-ensembl-motif-features/> gives more details on how we report motif features.
>  
> Best wishes,
> Anja
>  
> On 12 Mar 2020, at 12:53, Sigurjón Axel Guðjónsson <Sigurjon.Gudjonsson at decode.is <mailto:Sigurjon.Gudjonsson at decode.is>> wrote:
>  
>  
> Hi,
>  
> I am using VEP r99 to annotate i.e. rs759323910, and I notice that VEP only annotates MotifFeature ENSM00524563717 (ENSPFM0379). 
> The web browser does hower annotate 2 MotifFeatures ENSM00524563717 (ENSPFM0588) and ENSM00489900360 (ENSPFM0379). 
>  
> See:
> http://www.ensembl.org/Homo_sapiens/Variation/Mappings?db=core;v=rs759323910;vdb=variation <http://www.ensembl.org/Homo_sapiens/Variation/Mappings?db=core;v=rs759323910;vdb=variation>
>  
> Is there any valid reason for this discrepancy or is this a bug in VEP r99?
>  
> Best regards,
>  
> Sigurjon A. Gudjonsson
> Bioinformatics Group
> Decode Genetics
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