[ensembl-dev] Differences in Results - Core API vs Website (version 63)

[Bert Overduin]

Hello Simon,

Not all protein-coding transcript models have a 3' UTR. If you want to know which transcripts are protein-coding, ask for their biotype.

Cheers,
Bert

Sent from my iPhone

On Aug 2, 2011, at 8:15 PM, Simon Chan <sichan at bcgsc.ca> wrote:

> I wish to fetch all 3’ UTRs from the human genome using the latest version of the core API (version 63),  but I’m noticing some differences in the API results and what I see on the website.  ENSTs that return nothing from the ‘three_prime_utr’ method should be treated as non-protein coding RNAs.  For ENSG00000187634, the API reports that 3/9 transcripts have 3’UTR (as a result of being protein coding).  However, the website reports that 5/9 are protein coding.  (See here: http://uswest.ensembl.org/Homo_sapiens/Transcript/ProteinSummary?db=core;g=ENSG00000187634;r=1:860260-879955;t=ENST00000342066 )
> 
>  
> 
> My code and results are below.  Many thanks for any suggestions!
> 
> Simon.
> 
>  
> 
>  
> 
> #!/usr/bin/perl –w
> 
>  
> 
> use strict;
> 
> use Bio::EnsEMBL::Registry;
> 
>  
> 
> ###
> 
> ### Access the registry:
> 
> ###
> 
> my $registry = 'Bio::EnsEMBL::Registry';
> 
> $registry->load_registry_from_db(
> 
>         ### -host => 'ensembldb.ensembl.org',
> 
>         ### -user => 'anonymous'
> 
>         -host => 'ensembl01.bcgsc.ca',       
> 
>        -user => 'ensembl',
> 
>         -pass => 'ensembl',
> 
>         -port => 3306,
> 
>         -species => 'homo sapiens',
> 
>         -verbose => 0,
> 
>         -db_version => 63
> 
> );
> 
> my $gene_adaptor = $registry->get_adaptor('Human', 'Core', 'Gene');
> 
> my $gene_object  = $gene_adaptor->fetch_by_stable_id('ENSG00000187634');
> 
> my $all_trans    = $gene_object->get_all_Transcripts();
> 
> for my $trans_obj ( @{$all_trans} ){        
> 
>       my $ENST = $trans_obj->stable_id;
> 
>         my $thr_utr = $trans_obj->three_prime_utr;
> 
>         if (defined $thr_utr){
> 
>                 print "ENST:$ENST\t$thr_utr\n";
> 
>         } else {
> 
>                 print "ENST:$ENST\tNoUTR\n";
> 
>         }
> 
> }
> 
>  
> 
>  
> 
> ### Results:
> 
> ENST:ENST00000420190    NoUTR
> 
> ENST:ENST00000437963    NoUTR
> 
> ENST:ENST00000342066    Bio::Seq=HASH(0x182a1850)
> 
> ENST:ENST00000341065    Bio::Seq=HASH(0x183fb870)
> 
> ENST:ENST00000455979    Bio::Seq=HASH(0x182a0c40)
> 
> ENST:ENST00000478729    NoUTR
> 
> ENST:ENST00000474461    NoUTR
> 
> ENST:ENST00000466827    NoUTR
> 
> ENST:ENST00000464948    NoUTR
> 
>  
> 
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