[ensembl-dev] REST eQTL questions

[andrew126 at mac.com]

Hi Thomas,

Excellent .. thanks very much for the clarifications!

Best,

Andrew

> On Jan 27, 2017, at 11:39 AM, Thomas Juettemann <juettemann at ebi.ac.uk> wrote:
> 
> Hello Andrew,
> 
> my apologies for the delay in getting back to you and thank you for your interest in the eQTL data!
> Please find the answers inline, and don't hesitate to contact us again with question you may have, they are certainly not naive.
> 
> Best wishes,
> Thomas
> 
> 
> On 25 Jan 2017, at 02:26, andrew126 at mac.com wrote:
> 
> Hi,
> 
> Please forgive some naive REST eQTL questions.
> 
> The documentation says:
> 
> GET eqtl/stable_id/:species/:stable_id	Returns the p-value for each SNP in a given gene (e.g. ENSG00000227232)
> 1)
> How is “in a given gene” defined?
> 
> If I query REST for the homo sapiens gene in the example/documentation (ENSG00000227232) without any tissue or variant-name restrictions, then 159,122 of the returned results have a “display_consequence” of “intergenic_variant”, which is unexpected relative to “in a given gene”.
> 
> The counts for each different display_consequence are shown below:
> 
>   6366     'display_consequence' => '3_prime_UTR_variant'
>   1070     'display_consequence' => '5_prime_UTR_variant'
>  21006     'display_consequence' => 'downstream_gene_variant'
>      2     'display_consequence' => 'inframe_deletion'
> 159122     'display_consequence' => 'intergenic_variant'
> 186614     'display_consequence' => 'intron_variant'
>   1078     'display_consequence' => 'missense_variant'
>   6794     'display_consequence' => 'non_coding_transcript_exon_variant'
>     86     'display_consequence' => 'non_coding_transcript_variant'
>    634     'display_consequence' => 'splice_region_variant'
>    948     'display_consequence' => 'synonymous_variant'
>  21868     'display_consequence' => 'upstream_gene_variant'
> 
> The phrasing "in a given gene" is indeed incorrect and should be updated, thank you for pointing that out. It should have been: "Returns the p-value for each SNP around a given gene"
> 
> 
> 2)
> Whereas the documentation says that the stable gene id applies to the location of the eQTL SNP, and no gene information is returned in the result, am I to assume that the stable gene used for the query is also the gene in which the expression-level differences were observed (i.e. no trans effects can be recovered)?  
> 
> Correct
> 
> Will the result for the same SNP vary according to the query gene? 
> 
> Correct
> 
> That is, if a particular SNP is in the intergenic region between two oppositely oriented genes, it seems possible for that SNP to have a cis effect on both those genes.  To find such an occurrence, I would have to query by each gene separately?
> 
> Correct (or query the SNP)
> 
> 
> Thanks for any guidance.
> 
> Best regards,
> 
> Andrew
> 
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
> 
> 
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/