Data sources for V2G Scoring

General
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1

Hi there,

I am attempting to find all data sources included in the V2G scoring to understand it better, but the link to the full Data Sources set shows nothing. For example, I would like to see what the many sources for eQTLs and pQTLs are. Thanks.

2

Hi mjatoi,

Please see the subsections in Data sources for further details regarding each - in particular, this page explains the eQTL and pQTL sources. However, please bear in mind that V2G is no longer maintained and will be deprecated in the upcoming release.

Best wishes,
Xiangyu

3

Hi Xiangyu,

Thank you for your response. I am using V2G to see how SNPs are assigned genes on the platform. If I wanted to see that in the future, could I use L2G? Also, does L2G accept individual SNPs? When I try to search a SNP in Open Targets Genetics I see a search result but not in the Open Targets Platform, but is that accessible via the API?

Thanks.

4

Hi mjatoi,

Yes, you can use L2G for that purpose, it is an improvement over V2G in that the method aggregates information across all variants (V) found within a credible set (L) to predict target genes for the credible set.

Indeed, there is no variant search currently on the public Open Targets platform, but in the upcoming March release, you will be able to search by variant, and navigate to all credible sets which contains your variant of interest, and browse the L2G scores of gene assignments for each credible set.

Best wishes,
Xiangyu

5

Hi Xiangyu,

I appreciate the help! One more question for now: I understand that I can use a set of variants in a credible set to predict target genes for that set, but am I able to use similar schema for a single variant?

Thanks.