[ensembl-dev] REST eQTL questions
andrew126 at mac.com
andrew126 at mac.com
Wed Jan 25 02:26:37 GMT 2017
Hi,
Please forgive some naive REST eQTL questions.
The documentation says:
GET eqtl/stable_id/:species/:stable_id <http://rest.ensembl.org/documentation/info/species_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'
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)? Will the result for the same SNP vary according to the query gene? 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?
Thanks for any guidance.
Best regards,
Andrew
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