[ensembl-dev] Funcgen array mapping - Probeset with strange annotation result

Nathan Johnson njohnson at ebi.ac.uk
Thu Jan 13 16:17:22 GMT 2011


Hi Gavin

Not having mapped this probe set myself, I can't really tell what's going on.  Have you tried looking at the unmapped objects for these probes?  It could be that the other are 'promiscuous'.

Nath



On 12 Jan 2011, at 11:04, Oliver, Gavin wrote:

> Hi all,
>  
> One of our users has pointed out a probeset (affy utr format) that seems to be retrieving some unexpected annotation info via the FuncGen array mapping environment.
>  
> The probeset annotates to ENSG00000140853  but only seems to return probe features for four probes i.e. the end result says 4/11 probes align.  However when I look at the alignment manually using Ensembl or NCBI it looks like all probes align.  
>  
> To try and ensure that my scripts aren’t doing anything funny, I set up a quick test like this:
>  
> my @probes = @{$probeset->get_all_Probes};
>  
>         foreach my $probe (@probes) {
>                 my @probefeatures = @{$probe->get_all_ProbeFeatures()};
>                 foreach my $feature(@probefeatures) {
>                         print $feature->probe_id."\n";
>                 }
>         }
>  
> And sure enough only 4 probe IDs are returned.
>  
> The probes look like this:
>  
> >probe:ADXBRCv2a520413:BRRS.12588_at:1019:477; Interrogation_Position=313; Antisense;
> CCTGCCCTGGAAGTAATCTTGCTGT
> >probe:ADXBRCv2a520413:BRRS.12588_at:852:123; Interrogation_Position=324; Antisense;
> AGTAATCTTGCTGTCCTGGAATCTC
> >probe:ADXBRCv2a520413:BRRS.12588_at:665:993; Interrogation_Position=329; Antisense;
> TCTTGCTGTCCTGGAATCTCCTCGG
> >probe:ADXBRCv2a520413:BRRS.12588_at:295:809; Interrogation_Position=353; Antisense;
> GGGATGAGGCAGCTGCCGAGCTGGC
> >probe:ADXBRCv2a520413:BRRS.12588_at:921:949; Interrogation_Position=383; Antisense;
> TGCTGCCGAAGATGGGCCGGCTGAA
> >probe:ADXBRCv2a520413:BRRS.12588_at:1130:813; Interrogation_Position=478; Antisense;
> GGGTCTAGCATCCAAGTCATCCGCC
> >probe:ADXBRCv2a520413:BRRS.12588_at:411:539; Interrogation_Position=485; Antisense;
> GCATCCAAGTCATCCGCCTCTGGAA
> >probe:ADXBRCv2a520413:BRRS.12588_at:94:315; Interrogation_Position=491; Antisense;
> AAGTCATCCGCCTCTGGAATAACCC
> >probe:ADXBRCv2a520413:BRRS.12588_at:307:341; Interrogation_Position=508; Antisense;
> AATAACCCCATTCCCTGCGACATGG
> >probe:ADXBRCv2a520413:BRRS.12588_at:553:511; Interrogation_Position=524; Antisense;
> GCGACATGGCCCAGCACCTGAAGAG
> >probe:ADXBRCv2a520413:BRRS.12588_at:1099:419; Interrogation_Position=567; Antisense;
> CTTTGCCTTCTTTGACAACCAGCCC
>  
>  
> Can anyone suggest what might be happening?
>  
> Best,
>  
> Gavin
>  
>  
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Nathan Johnson
Scientific Programmer
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
Email: njohnson at ebi.ac.uk
TelNo: (+44)1223 492629





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