[ensembl-dev] associated or reported gene for phenotypes

[Will McLaren]

Hi Mark,

You could use either a MySQL query on the variation database (
homo_sapiens_variation_84_38 at ensembldb.ensembl.org:3306):

SELECT pf.*, pfa.value AS associated_gene
FROM phenotype_feature pf, phenotype p, phenotype_feature_attrib pfa,
attrib_type a
WHERE pf.phenotype_id = p.phenotype_id
AND pf.phenotype_feature_id = pfa.phenotype_feature_id
AND pfa.attrib_type_id = a.attrib_type_id
AND a.code = 'associated_gene'
AND p.description = 'DIABETES MELLITUS, TYPE 2';

or the perl API; you'd need to fetch a phenotype object and then all
associated phenotype features, filtering that list down to those with
associated genes. Here's some links with a tutorial and the relevant class
documentation:

http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#phenotype
http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1DBSQL_1_1PhenotypeAdaptor.html
http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1DBSQL_1_1PhenotypeFeatureAdaptor.html

Regards

Will McLaren
Ensembl Variation


On 21 April 2016 at 22:00, William Spooner <
william.spooner at eaglegenomics.com> wrote:

> Hi Mark,
>
> Ensembl only explicitly associates a gene with a variant when it is
> within 5kb upstream/downstream. Your SNP is outside this range. You
> can query for SNPs that are outside this range by calculating the
> location and using BioMart or the Ensembl Perl API. Direct SQL is not
> guaranteed to work.
>
> Best,
>
> Will
>
> On Thu, Apr 21, 2016 at 8:36 PM, Mark Miller <Mark.Miller at instem.com>
> wrote:
> > How can I programmatically retrieve variants that are associated with a
> > phenotype and ASSOCIATED with a gene, even if the variant is not strictly
> > within a gene’s boundaries?
> >
> >
> >
> > If you visit
> >
> http://useast.ensembl.org/Homo_sapiens/Gene/Phenotype?db=core;g=ENSG00000073756;r=1:186671791-186680427#ALL_tablePanel
> ,
> > under “ALL associated variants” you will see rs10489403 associated with
> > hematocrit phenotypes.
> >
> >
> >
> > If I query biomart for variants and phenotypes associated with
> > ENSG00000073756, rs10489403 is not listed.
> >
> >         <Dataset name = "hsapiens_snp" interface = "default" >
> >
> >                <Filter name = "ensembl_gene" value = "ENSG00000073756"/>
> >
> >                <Attribute name = "refsnp_id" />
> >
> >                <Attribute name = "ensembl_gene_stable_id" />
> >
> >                <Attribute name = "associated_gene" />
> >
> >         </Dataset>
> >
> >
> >
> > If I look for rs10489403 in the web interface or biomart, I see that it
> is
> > intergenic between PGTS2 and PLA2G4A.
> >
> >         <Dataset name = "hsapiens_snp" interface = "default" >
> >
> >                <Filter name = "snp_filter" value = "rs10489403"/>
> >
> >                <Attribute name = "refsnp_id" />
> >
> >                <Attribute name = "ensembl_gene_stable_id" />
> >
> >                <Attribute name = "associated_gene" />
> >
> >         </Dataset>
> >
> >
> >
> > It doesn’t seem like associated_gene  is a filterable field.  How can I
> > query biomart, or MySQL directly,  with ENSG00000073756 as my gene of
> > interest and retrieve rs10489403 as a variant which has PTGS2/
> > ENSG00000073756 as an associated gene?
> >
> >
> >
> > Thanks,
> >
> > Mark
> >
> >
> >
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