[ensembl-dev] eQTL API fetch results don't match those on GTEx website

Shraddha Pai shraddhapai.neuro at gmail.com
Thu Nov 22 15:54:18 GMT 2018


Hello Ensembl dev community,

I used the Ensembl REST API for the first time yesterday, to fetch eQTL
results associated with a set of SNPs. But the results I get from the
Ensembl API don't match those from a manual query I performed on the GTEx
website.

I used this endpoint: GET eqtl/variant_name/:species/:variant_name
<http://rest.ensembl.org/documentation/info/species_variant>
http://rest.ensembl.org/documentation/info/species_variant
Isn't GTEx the source for these eQTL associations?

Here is the snippet of Perl code I used to fetch results for a snp:
---
    print "$snp\n";

    my $ping_endpoint = "/eqtl/variant_name/homo_sapiens/$snp";
    my $url = $server.$ping_endpoint;
    my $response = rest_request($url, $headers);
    for my $cur ( @{ $response }) {
        my $tis=$cur->{tissue};
        my $val=$cur->{value};
        my $gene=$cur->{gene};
        my $statistic=$cur->{statistic};
        if  ($statistic=~/p-value/) {
            print OUT "$snp\t$tis\t$gene\t$statistic\t$val\n";
        }
    }
close(OUT) || die "$!";
---

As an example, according to my API call, the only significant eQTL for
rs11703062 is this:
rs11703062  Adipose_Visceral_Omentum    ENSG00000100376 p-value
0.0289612051829416

But the GTex page lists many more (see "significant eGenes" table in
screenshot).
[image: Screen Shot 2018-11-22 at 10.49.34 AM.png]

What am I missing here?

Thanks!
Shraddha
----
Shraddha Pai
Post-doctoral Fellow, http://baderlab.org
The Donnelly Center, University of Toronto
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20181122/64ad5645/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screen Shot 2018-11-22 at 10.49.34 AM.png
Type: image/png
Size: 210526 bytes
Desc: not available
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20181122/64ad5645/attachment.png>


More information about the Dev mailing list