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Hi Nathalie,<br>
<br>
You are extracting phenotype features for the input mouse gene, not
the human gene, which is why you are not seeing the human phenotype
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
128257628 1 <br>
gene is Lep ENSMUSG00000059201 scalar 0<br>
no PHE<br>
<br>
<br>
<br>
We store associations as reported, so querying by both gene and
variant will return the most complete set of results<br>
<br>
fetch_all_by_Gene takes a gene object and returns associations
reported to the gene<br>
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charset=windows-1252">
fetch_all_by_associated_gene() takes a gene name and returns variant
associations in which it is mentioned<br>
<br>
<br>
For example:<br>
<br>
use Bio::EnsEMBL::Registry;<br>
<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>
<br>
my $ga = Bio::EnsEMBL::Registry->get_adaptor("homo_sapiens",
"core", "gene");<br>
my $pfh_adaptor = Bio::EnsEMBL::Registry->get_adaptor('human',
'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
"Direct\t",$pm->source_name,"\t",$pm->phenotype->description,
"\n";<br>
}<br>
<br>
my $pfsvar =
$pfh_adaptor->fetch_all_by_associated_gene($gene->external_name());<br>
foreach my $pmv(@{$pfsvar}){<br>
print
"Assoc\t",$pmv->source_name,"\t",$pmv->phenotype->description,
"\n";<br>
}<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
description is publicly available<br>
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype
description is publicly available<br>
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype
description is publicly available<br>
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype
description is publicly available<br>
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype
description is publicly available<br>
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype
description is publicly available<br>
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype
description is publicly available<br>
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype
description is publicly available<br>
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype
description is publicly available<br>
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype
description is publicly available<br>
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype
description is publicly available<br>
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype
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>
<br>
Best wishes,<br>
<br>
Sarah<br>
<br>
<div class="moz-cite-prefix">On 26/02/2016 12:50, nconte wrote:<br>
</div>
<blockquote
cite="mid:20160226125117.E3EC222F1E8_6D04A45B@hx-mx1.ebi.ac.uk"
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>
<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>
<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>
<br>
script:
<br>
#!/usr/local/bin/perl
<br>
use strict;
<br>
use warnings;
<br>
use DBI;
<br>
use Bio::EnsEMBL::Registry;
<br>
<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>
<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>
<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
method\n"; ##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) &&
$homgene->genome_db->name eq "homo_sapiens") {
<br>
<br>
<br>
print join("\t", "human Orthologue:
".$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>
<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
PHE\n";}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>
<br>
} else{next;}
<br>
<br>
<br>
<br>
<br>
}else {print 'no gene member',"\n"};
<br>
<br>
<br>
__END__
<br>
<br>
<br>
<br>
<br>
<br>
<br>
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<br>
</blockquote>
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