[Bioperl-l] Converting Human GeneID to Mouse GeneID

Chris Fields cjfields at uiuc.edu
Fri Nov 17 13:51:27 EST 2006


On Nov 17, 2006, at 8:59 AM, Cui, Wenwu ((NIH/NLM/NCBI)) [C] wrote:

> You can query HomoloGene DB using NCBI EUtils:
>
> ESearch like this:
> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi? 
> db=homologene&
> term=BRCA1[gene%20name]&retmode=text
>
> Once get HomoloGene id then
> Then Efetch:
> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi? 
> db=homologene&i
> d=5276
>
> Just SOAP it to get the gi and acc via taxid.
>
> Good luck.
>
> Wenwu Cui
>
>
> -----Original Message-----
> From: Paul Cantalupo [mailto:pcantalupo at gmail.com]
> Sent: Thursday, November 16, 2006 11:27 AM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Converting Human GeneID to Mouse GeneID
>
> Hello,
>
> Is there a way with Bioperl (or some other tool - NCBI EUtils?) to
> convert a
> Human NCBI GeneID to a Mouse GeneID. I have a list of Human GeneID's
> that I
> need to convert to Mouse GeneIDs so that I can compare them to my  
> Mouse
> microarray data.
>
> Thank you,
>
> Paul
> ...

You could also use esearch(homologene, using history)->elink 
(homologene_gene, using history)->esummary(elink 'cookie').

I have set up a (very) experimental BioPerl interface to NCBI eutils  
(Bio::DB::EUtilities).  If you update from CVS (this won't be in the  
1.5.2 release), you could do something like this:

------------------------------------------------------
use Bio::DB::EUtilities;
my $term = 'BRCA1[gene name]';
# grab BRCA1 homologene UID
my $esearch = Bio::DB::EUtilities->new(-eutil => 'esearch',
                                        -db  => 'homologene',
                                        -term  => $term,
                                        -usehistory => 'y');

$esearch->get_response;

my @h_genes = $esearch->get_ids;

# what Gene UIDs are linked to the Homologene UID?
my $elink = Bio::DB::EUtilities->new(-eutil => 'elink',
                                       -db  => 'gene',
                                       -cookie => $esearch->next_cookie,
                                       -cmd => 'neighbor_history');

$elink->get_response;

# what taxids go with which GeneID?
my $esum = Bio::DB::EUtilities->new(-eutil => 'esummary',
                                     -cookie => $elink->next_cookie);

$esum->get_response;

while (my $docsum = $esum->next_docsum) {
     print $docsum->esummary_id,"\n";
     print "\t\tTaxID: ",$docsum->get_Content_by_name('TaxID'),"\n";
     print "\t\tOrganism: ",$docsum->get_Content_by_name 
('Orgname'),"\n";
}

------------------------------------------------------

A future bioperl SOAP interface for eutils is also not out of the  
question either, just haven't had time to play around with it.

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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