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<br>
Hi Nathalie,<br>
<br>
There are duplicates because all variant associations are reported.
If you look at the table given by the
<meta http-equiv="content-type" content="text/html; charset=utf-8">
'Show' option on 'ALL variants with a phenotype annotation' on the
web page you will see multiple variants sometimes have reported
associations to the same trait. In one case multiple associations
are reported at different levels of significance between a variant
and a trait.<br>
<br>
Full HGMD data is only available to registered users, so Ensembl can
only report the presence of a variant location in the HGMD database.
ClinVar accepts submissions with different levels of information, so
it is sometimes only reported that a variant is pathogenic but no
phenotype is available.<br>
<br>
If you are not interested in significance levels and undescribed
phenotypes, they should be simple to filter out.<br>
<br>
Best wishes,<br>
<br>
Sarah<br>
<br>
<div class="moz-cite-prefix">On 26/02/2016 16:42, nconte wrote:<br>
</div>
<blockquote cite="mid:08c138437a1ad7df85193dbc998426e7@ebi.ac.uk"
type="cite">Hi Sarah,
<br>
Another question when the script show phenotypes there will be
some duplicate (see below), why is this ?
<br>
and why some have phenotype is not specified (clinvar) or not
avalaible (like with HMGD)? and how to remove these like in the
website ?
<br>
<a class="moz-txt-link-freetext" href="http://www.ensembl.org/Homo_sapiens/Gene/Phenotype?db=core;g=ENSG00000115963;r=2:150468195-150539011">http://www.ensembl.org/Homo_sapiens/Gene/Phenotype?db=core;g=ENSG00000115963;r=2:150468195-150539011</a>
<br>
<br>
many thanks
<br>
<br>
<br>
my $gene = $ga->fetch_by_stable_id('ENSG00000115963');
<br>
this is an example with
<br>
human Orthologue: RND3 ENSG00000115963 2 150468195
150539011 -1
<br>
gene is RND3ENSG00000115963
<br>
Assoc ClinVar ClinVar: phenotype not specified
<br>
Assoc ClinVar ClinVar: phenotype not specified
<br>
Assoc ClinVar ClinVar: phenotype not specified
<br>
Assoc ClinVar ClinVar: phenotype not specified
<br>
Assoc ClinVar ClinVar: phenotype not specified
<br>
Assoc ClinVar ClinVar: phenotype not specified
<br>
Assoc dbGaP Blood pressure
<br>
Assoc dbGaP Body Height
<br>
Assoc dbGaP Body Height
<br>
Assoc dbGaP Body Height
<br>
Assoc dbGaP Body Height
<br>
Assoc dbGaP Body Height
<br>
Assoc dbGaP Body Height
<br>
Assoc dbGaP Body Height
<br>
Assoc dbGaP Body Height
<br>
Assoc dbGaP Body Height
<br>
Assoc dbGaP Body Height
<br>
Assoc dbGaP Body Height
<br>
Assoc dbGaP Body Height
<br>
Assoc dbGaP BODY MASS INDEX
<br>
Assoc dbGaP BODY MASS INDEX
<br>
Assoc dbGaP BODY MASS INDEX
<br>
Assoc dbGaP BODY MASS INDEX
<br>
Assoc dbGaP Calcium
<br>
Assoc dbGaP Calcium
<br>
Assoc dbGaP Cholesterol, HDL
<br>
Assoc dbGaP Glucose
<br>
Assoc dbGaP Respiration Disorders
<br>
Assoc dbGaP Sleep
<br>
Assoc dbGaP Stroke
<br>
Assoc NHGRI-EBI GWAS catalog Endometriosis
<br>
Assoc NHGRI-EBI GWAS catalog Type 2 diabetes
<br>
<br>
<br>
<br>
<br>
> Hi Nathalie,
<br>
<blockquote type="cite">
<br>
You are extracting phenotype features for the input mouse gene,
not
<br>
the human gene, which is why you are not seeing the human
phenotype
<br>
feature. If you change the print statement to:
<br>
<br>
print 'gene is '.$gene->external_name() ." ".
$gene->stable_id();
<br>
<br>
You will see the 'ENSMUS' prefix on the gene name:
<br>
<br>
human Orthologue: LEP ENSG00000174697 7 128241284
<br>
128257628 1
<br>
gene is Lep ENSMUSG00000059201 scalar 0
<br>
no PHE
<br>
<br>
We store associations as reported, so querying by both gene and
<br>
variant will return the most complete set of results
<br>
<br>
fetch_all_by_Gene takes a gene object and returns associations
<br>
reported to the gene
<br>
fetch_all_by_associated_gene() takes a gene name and returns
variant
<br>
associations in which it is mentioned
<br>
<br>
For example:
<br>
<br>
use Bio::EnsEMBL::Registry;
<br>
<br>
Bio::EnsEMBL::Registry->load_registry_from_db(
<br>
-host=> 'ensembldb.ensembl.org', -user=>'anonymous',
<br>
-port=>'3306', 'db_version' => 83,);
<br>
Bio::EnsEMBL::Registry->set_reconnect_when_lost(1);# will
help with
<br>
connection issues
<br>
<br>
my $ga = Bio::EnsEMBL::Registry->get_adaptor("homo_sapiens",
"core", "gene");
<br>
my $pfh_adaptor =
Bio::EnsEMBL::Registry->get_adaptor('human',
<br>
'variation', 'phenotypefeature');
<br>
<br>
my $gene = $ga->fetch_by_stable_id('ENSG00000174697');
<br>
<br>
if ($gene){
<br>
print "gene is " .$gene->external_name() ."n";
<br>
<br>
my $pfs = $pfh_adaptor->fetch_all_by_Gene($gene);
<br>
foreach my $pm(@{$pfs}){
<br>
print
"Directt",$pm->source_name,"t",$pm->phenotype->description,
"n";
<br>
}
<br>
<br>
my $pfsvar =
<br>
$pfh_adaptor->fetch_all_by_associated_gene($gene->external_name());
<br>
foreach my $pmv(@{$pfsvar}){
<br>
print
"Assoct",$pmv->source_name,"t",$pmv->phenotype->description,
"n";
<br>
}
<br>
}
<br>
<br>
Outputs:
<br>
<br>
gene is LEP
<br>
Direct Orphanet Obesity due to congenital leptin
deficiency
<br>
Direct MIM morbid LEPTIN DEFICIENCY OR DYSFUNCTION
<br>
Assoc ClinVar ClinVar: phenotype not specified
<br>
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype
<br>
description is publicly available
<br>
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype
<br>
description is publicly available
<br>
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype
<br>
description is publicly available
<br>
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype
<br>
description is publicly available
<br>
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype
<br>
description is publicly available
<br>
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype
<br>
description is publicly available
<br>
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype
<br>
description is publicly available
<br>
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype
<br>
description is publicly available
<br>
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype
<br>
description is publicly available
<br>
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype
<br>
description is publicly available
<br>
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype
<br>
description is publicly available
<br>
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype
<br>
description is publicly available
<br>
Assoc Uniprot Leptin deficiency
<br>
Assoc OMIM LEPTIN DYSFUNCTION
<br>
Assoc OMIM Leptin deficiency
<br>
Assoc ClinVar LEPTIN DYSFUNCTION
<br>
Assoc ClinVar Obesity, severe, due to leptin deficiency
<br>
Assoc dbGaP Blood pressure
<br>
Assoc dbGaP Erythrocyte Count
<br>
Assoc NHGRI-EBI GWAS catalog Type 2 diabetes
<br>
Assoc dbGaP Amyotrophic lateral sclerosis
<br>
Assoc ClinVar ClinVar: phenotype not specified
<br>
Assoc ClinVar ClinVar: phenotype not specified
<br>
<br>
Best wishes,
<br>
<br>
Sarah
<br>
<br>
On 26/02/2016 12:50, nconte wrote:
<br>
<br>
<blockquote type="cite">Hello
<br>
I have an issue with phenotypeFeature fetch_all_by_Gene($gene)
method. I am trying to retrieve phenotype from gene object and
the script I have doesn't find any phenotype relating to this
gene, whereas the ensembl website shows some phenotype linked
with gene
<br>
<a class="moz-txt-link-freetext" href="http://www.ensembl.org/Homo_sapiens/Gene/Phenotype?db=core;g=ENSG00000174697;r=7:128241284-128257628;t=ENST00000308868">http://www.ensembl.org/Homo_sapiens/Gene/Phenotype?db=core;g=ENSG00000174697;r=7:128241284-128257628;t=ENST00000308868</a>
[1]
<br>
<br>
my starting point is a mouse gene from which i retrieve the
human orthologue, and then query the phenotype related to this
orthologue.
<br>
the script below should work and print no PHE for human LEP
gene whereas there are phenotype linked to gene according to
website
<br>
output:
<br>
human Orthologue: LEP ENSG00000174697 7 128241284
128257628 1
<br>
gene is Lep scalar 0
<br>
no PHE
<br>
<br>
any advise would be great - Also is it better to find
phenotypes relating to variation of a gene rather than to the
gene itself in order to get the full picture of phenotype
related to a specific gene?
<br>
thanks
<br>
Nathalie
<br>
<br>
script:
<br>
#!/usr/local/bin/perl
<br>
use strict;
<br>
use warnings;
<br>
use DBI;
<br>
use Bio::EnsEMBL::Registry;
<br>
<br>
Bio::EnsEMBL::Registry->load_registry_from_db(
<br>
-host=> 'ensembldb.ensembl.org',
-user=>'anonymous',
<br>
-port=>'3306', 'db_version' => 83,);
<br>
Bio::EnsEMBL::Registry->set_reconnect_when_lost(1);# will
help with connection issues
<br>
<br>
my $gene_member_adaptor=
Bio::EnsEMBL::Registry->get_adaptor("Multi", "compara",
"GeneMember");
<br>
my $homology_adaptor =
Bio::EnsEMBL::Registry->get_adaptor("Multi", "compara",
"Homology");
<br>
my $pfh_adaptor =
Bio::EnsEMBL::Registry->get_adaptor('human', 'variation',
'phenotypefeature');
<br>
<br>
my $gene_member =
$gene_member_adaptor->fetch_by_stable_id('ENSMUSG00000059201');
<br>
#get the ensembl object correspoding to this mouse stable ID
<br>
<br>
if ($gene_member){
<br>
<br>
#get orthologues in human
<br>
my $all_homologies =
$homology_adaptor->fetch_all_by_Member($gene_member,
-TARGET_SPECIES => 'homo_sapiens',-METHOD_LINK_TYPE =>
'ENSEMBL_ORTHOLOGUES');
<br>
if (!scalar(@{$all_homologies})){
<br>
<br>
print "no orthologue with ensembl orthology
methodn"; ##1
<br>
} # print a message if there is no
corresponding mouse orthologue
<br>
else{
<br>
#if there is/are orthologue(s) ,find them and print
annotation about these
<br>
foreach my $this_homology
(@{$all_homologies}){
<br>
my $homologue_genes =
$this_homology->gene_list();
<br>
my $homgene;
<br>
foreach $homgene(@{$homologue_genes}){
<br>
#get human orthologues only
<br>
if (defined
($homgene->genome_db->name) &&
$homgene->genome_db->name eq "homo_sapiens") {
<br>
<br>
print join("t", "human
Orthologue:
".$homgene->display_label,$homgene->stable_id,$homgene->dnafrag()->name(),
$homgene->dnafrag_start,$homgene->dnafrag_end,$homgene->dnafrag_strand,
"n" ) ;
<br>
<br>
}
<br>
<br>
}
<br>
}
<br>
}
<br>
<br>
my $gene = $gene_member->get_Gene();
<br>
<br>
if ($gene){
<br>
print 'gene is
'.$gene->external_name();
<br>
my $pfs =
$pfh_adaptor->fetch_all_by_Gene($gene);
<br>
print "t", 'scalar '.scalar(@$pfs), "n";
<br>
if ( scalar(@$pfs)== 0 ){print "no
PHEn";}else{
<br>
foreach my $pm(@{$pfs}){
<br>
if ($pm){
<br>
<br>
#fill with info about ensembl gene
phenotype
<br>
<br>
print
"t",$pm->source_name,"t",$pm->phenotype->description,
"n";
<br>
}else {next;}
<br>
}
<br>
}
<br>
<br>
} else{next;}
<br>
<br>
}else {print 'no gene member',"n"};
<br>
<br>
__END__
<br>
<br>
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Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a> [3]
<br>
</blockquote>
<br>
<br>
<br>
Links:
<br>
------
<br>
[1]
<br>
<a class="moz-txt-link-freetext" href="http://www.ensembl.org/Homo_sapiens/Gene/Phenotype?db=core;g=ENSG00000174697;r=7:128241284-128257628;t=ENST00000308868">http://www.ensembl.org/Homo_sapiens/Gene/Phenotype?db=core;g=ENSG00000174697;r=7:128241284-128257628;t=ENST00000308868</a>
<br>
[2] <a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
<br>
[3] <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
<br>
<br>
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Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
<br>
</blockquote>
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