Hey Everyone! I’m trying to replicate the associated studies table from OpenTargets (Example of GRN gene Open Targets Genetics) via BigQuery. Is it possible to get the exact columns that are there via only joining datasets from OpenTargets genetics table.
Hi @hrant and welcome to our Community!
The associated studies sections mainly come from 2 different datasets:
- Results derived from locus-to-gene come from asking the question in the opposite way as we usually formulate it: given we have inferred the likely causal gene from an association between a trait (study), and a locus, if I fix GRN, what are the studies that are linked to it?
To replicate the table, you want to merge data from our L2G dataset and the V2D dataset, where the metadata about the association signal is located. - Results derived from colocalisation inform about other studies that share the same causal variant. Here we only look at mQTL studies because the measured trait is a gene product.
To replicate the table, use our colocalisation dataset. Here you have comparisons between pairs of associations. You will always find the data about the QTL study (and therefore the associated gene) on the right.
Sorry for the late reply, I hope this is still useful.
Best,
Irene
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