[ensembl-dev] Issues with phenotypeFeature
Sarah Hunt
seh at ebi.ac.uk
Fri Feb 26 14:00:30 GMT 2016
Hi Nathalie,
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:
print 'gene is '.$gene->external_name() ." ". $gene->stable_id();
You will see the 'ENSMUS' prefix on the gene name:
human Orthologue: LEP ENSG00000174697 7 128241284 128257628 1
gene is Lep ENSMUSG00000059201 scalar 0
no PHE
We store associations as reported, so querying by both gene and variant
will return the most complete set of results
fetch_all_by_Gene takes a gene object and returns associations reported
to the gene
fetch_all_by_associated_gene() takes a gene name and returns variant
associations in which it is mentioned
For example:
use Bio::EnsEMBL::Registry;
Bio::EnsEMBL::Registry->load_registry_from_db(
-host=> 'ensembldb.ensembl.org', -user=>'anonymous',
-port=>'3306', 'db_version' => 83,);
Bio::EnsEMBL::Registry->set_reconnect_when_lost(1);# will help with
connection issues
my $ga = Bio::EnsEMBL::Registry->get_adaptor("homo_sapiens", "core",
"gene");
my $pfh_adaptor = Bio::EnsEMBL::Registry->get_adaptor('human',
'variation', 'phenotypefeature');
my $gene = $ga->fetch_by_stable_id('ENSG00000174697');
if ($gene){
print "gene is " .$gene->external_name() ."\n";
my $pfs = $pfh_adaptor->fetch_all_by_Gene($gene);
foreach my $pm(@{$pfs}){
print "Direct\t",$pm->source_name,"\t",$pm->phenotype->description,
"\n";
}
my $pfsvar =
$pfh_adaptor->fetch_all_by_associated_gene($gene->external_name());
foreach my $pmv(@{$pfsvar}){
print
"Assoc\t",$pmv->source_name,"\t",$pmv->phenotype->description, "\n";
}
}
Outputs:
gene is LEP
Direct Orphanet Obesity due to congenital leptin deficiency
Direct MIM morbid LEPTIN DEFICIENCY OR DYSFUNCTION
Assoc ClinVar ClinVar: phenotype not specified
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype description
is publicly available
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype description
is publicly available
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype description
is publicly available
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype description
is publicly available
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype description
is publicly available
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype description
is publicly available
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype description
is publicly available
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype description
is publicly available
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype description
is publicly available
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype description
is publicly available
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype description
is publicly available
Assoc HGMD-PUBLIC Annotated by HGMD but no phenotype description
is publicly available
Assoc Uniprot Leptin deficiency
Assoc OMIM LEPTIN DYSFUNCTION
Assoc OMIM Leptin deficiency
Assoc ClinVar LEPTIN DYSFUNCTION
Assoc ClinVar Obesity, severe, due to leptin deficiency
Assoc dbGaP Blood pressure
Assoc dbGaP Erythrocyte Count
Assoc NHGRI-EBI GWAS catalog Type 2 diabetes
Assoc dbGaP Amyotrophic lateral sclerosis
Assoc ClinVar ClinVar: phenotype not specified
Assoc ClinVar ClinVar: phenotype not specified
Best wishes,
Sarah
On 26/02/2016 12:50, nconte wrote:
> Hello
> 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
> http://www.ensembl.org/Homo_sapiens/Gene/Phenotype?db=core;g=ENSG00000174697;r=7:128241284-128257628;t=ENST00000308868
>
>
> my starting point is a mouse gene from which i retrieve the human
> orthologue, and then query the phenotype related to this orthologue.
> the script below should work and print no PHE for human LEP gene
> whereas there are phenotype linked to gene according to website
> output:
> human Orthologue: LEP ENSG00000174697 7 128241284 128257628 1
> gene is Lep scalar 0
> no PHE
>
>
> 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?
> thanks
> Nathalie
>
>
> script:
> #!/usr/local/bin/perl
> use strict;
> use warnings;
> use DBI;
> use Bio::EnsEMBL::Registry;
>
>
> Bio::EnsEMBL::Registry->load_registry_from_db(
> -host=> 'ensembldb.ensembl.org', -user=>'anonymous',
> -port=>'3306', 'db_version' => 83,);
> Bio::EnsEMBL::Registry->set_reconnect_when_lost(1);# will help with
> connection issues
>
>
> my $gene_member_adaptor= Bio::EnsEMBL::Registry->get_adaptor("Multi",
> "compara", "GeneMember");
> my $homology_adaptor = Bio::EnsEMBL::Registry->get_adaptor("Multi",
> "compara", "Homology");
> my $pfh_adaptor = Bio::EnsEMBL::Registry->get_adaptor('human',
> 'variation', 'phenotypefeature');
>
>
> my $gene_member =
> $gene_member_adaptor->fetch_by_stable_id('ENSMUSG00000059201');
> #get the ensembl object correspoding to this mouse stable ID
>
> if ($gene_member){
>
> #get orthologues in human
> my $all_homologies =
> $homology_adaptor->fetch_all_by_Member($gene_member, -TARGET_SPECIES
> => 'homo_sapiens',-METHOD_LINK_TYPE => 'ENSEMBL_ORTHOLOGUES');
> if (!scalar(@{$all_homologies})){
>
> print "no orthologue with ensembl orthology
> method\n"; ##1
> } # print a message if there is no corresponding
> mouse orthologue
> else{
> #if there is/are orthologue(s) ,find them and print annotation
> about these
> foreach my $this_homology (@{$all_homologies}){
> my $homologue_genes = $this_homology->gene_list();
> my $homgene;
> foreach $homgene(@{$homologue_genes}){
> #get human orthologues only
> if (defined ($homgene->genome_db->name) &&
> $homgene->genome_db->name eq "homo_sapiens") {
>
>
> print join("\t", "human Orthologue:
> ".$homgene->display_label,$homgene->stable_id,$homgene->dnafrag()->name(),
> $homgene->dnafrag_start,$homgene->dnafrag_end,$homgene->dnafrag_strand, "\n"
> ) ;
>
> }
>
> }
> }
> }
>
>
> my $gene = $gene_member->get_Gene();
>
> if ($gene){
> print 'gene is '.$gene->external_name();
> my $pfs = $pfh_adaptor->fetch_all_by_Gene($gene);
> print "\t", 'scalar '.scalar(@$pfs), "\n";
> if ( scalar(@$pfs)== 0 ){print "no PHE\n";}else{
> foreach my $pm(@{$pfs}){
> if ($pm){
>
> #fill with info about ensembl gene phenotype
>
> print
> "\t",$pm->source_name,"\t",$pm->phenotype->description, "\n";
> }else {next;}
> }
> }
>
>
> } else{next;}
>
>
>
>
> }else {print 'no gene member',"\n"};
>
>
> __END__
>
>
>
>
>
>
> _______________________________________________
> Dev mailing list Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20160226/89b64c3d/attachment.html>
More information about the Dev
mailing list