[ensembl-dev] probe mapping for transcripts
Nathan Johnson
njohnson at ebi.ac.uk
Fri Jun 24 16:49:10 BST 2011
Hi Eduardo
Just for completeness, and anyone else pondering the answer to this, I am replying in brief, to the list also.
As I said, the problem here is that you need to look at the probe level for non-affy arrays. Transcript xrefs are associated with probesets for affy arrays and probes for non-affy arrays.
Thanks
Nath
On 17 Jun 2011, at 11:44, Eduardo Andrés León wrote:
> Dear all,
>
> I'm using this code :
>
> my $tx_adaptor = $registry->get_adaptor("human","core","Transcript");
> my $ps_adaptor = $registry->get_adaptor("human","funcgen","ProbeSet");
>
> #Fetch the transcript and associated ProbeSets
> my $transcript = $tx_adaptor->fetch_by_stable_id(ENST00000381223);
> my @probesets = @{$ps_adaptor->fetch_all_by_external_name($transcript->stable_id)};
> foreach my $probeset (@probesets){
> my $arrays = $probeset->get_all_Arrays();
> foreach my $probe (@$arrays){
> print "\t". $probeset->name ."\t" . $probe->name() ."\n";
> }
> }
>
> To find all probes related with a transcript (for example : ENST00000381223) .
>
> in the page , the results is something like :
>
> http://www.ensembl.org/Homo_sapiens/Transcript/Oligos?db=core;g=ENSG00000214717;r=X:2404455-2419008;t=ENST00000381223
>
> where 11 platforms are found :
>
> This transcript corresponds to the following database identifiers:
> AFFY HG-U133_Plus_2:
> 1554821_a_at[11/11 in probeset. Matches 2 other transcripts] [view all locations]
> 203043_at[9/11 in probeset. Matches 2 other transcripts] [view all locations]
> AFFY HG-U95A:
> 39168_at[16/16 in probeset. Matches 2 other transcripts] [view all locations]
> AFFY HG-U95B:
> 44978_at[16/16 in probeset. Matches 2 other transcripts] [view all locations]
> AFFY HuEx-1_0-st-v2:
> 3997567[4/4 in probeset. Matches 2 other transcripts] [view all locations]
> 3997568[4/4 in probeset. Matches 2 other transcripts] [view all locations]
> 3997569[4/4 in probeset. Matches 2 other transcripts] [view all locations]
> 3997570[4/4 in probeset. Matches 3 other transcripts] [view all locations]
> 3997571[4/4 in probeset. Matches 3 other transcripts] [view all locations]
> 3997575[4/4 in probeset. Matches 6 other transcripts] [view all locations]
> 3997576[4/4 in probeset. Matches 6 other transcripts] [view all locations]
> 4033358[4/4 in probeset. Matches 2 other transcripts] [view all locations]
> 4033359[4/4 in probeset. Matches 2 other transcripts] [view all locations]
> 4033360[4/4 in probeset. Matches 2 other transcripts] [view all locations]
> 4033361[4/4 in probeset. Matches 3 other transcripts] [view all locations]
> 4033362[3/3 in probeset. Matches 3 other transcripts] [view all locations]
> 4033365[4/4 in probeset. Matches 6 other transcripts] [view all locations]
> AFFY HuGene-1_0-st-v1:
> 8171139[32/42 in probeset. Matches 2 other transcripts] [view all locations]
> 8177029[22/42 in probeset. Matches 2 other transcripts] [view all locations]
> AFFY U133_X3P:
> Hs2.9933.2.S1_3p_x_at[11/11 in probeset. Matches 2 other transcripts] [view all locations]
> g4759257_3p_at[9/11 in probeset. Matches 2 other transcripts] [view all locations]
> AGILENT WholeGenome:
> A_23_P217507[Matches exon/3' flank boundary. Matches 2 other transcripts] [view all locations]
> A_32_P86623[Matches exon/3' flank boundary. Matches 2 other transcripts] [view all locations]
> CODELINK:
> GE53488[Matches 3' flank. Matches 2 other transcripts] [view all locations]
> ILLUMINA HumanWG_6_V2:
> ILMN_1694466[Matches 3' flank. Matches 2 other transcripts] [view all locations]
> PHALANX OneArray:
> PH_hs_0026388[Matches exon/3' flank boundary. Matches 2 other transcripts] [view all locations]
>
> But in my case only
>
> 44978_at HG-U95B
> 39168_at HG-U95Av2
> 39168_at HG-U95A
> Hs2.9933.2.S1_3p_x_at U133_X3P
> 203043_at HG-Focus
> 203043_at HG-U133A_2
> 203043_at HG-U133A
> 203043_at HG-U133_Plus_2
> g4759257_3p_at U133_X3P
> 1554821_a_at HG-U133_Plus_2
> 3997575 HuEx-1_0-st-v2
> 3997569 HuEx-1_0-st-v2
> 3997571 HuEx-1_0-st-v2
> 3997568 HuEx-1_0-st-v2
> 3997570 HuEx-1_0-st-v2
> 4033360 HuEx-1_0-st-v2
> 4033365 HuEx-1_0-st-v2
> 4033359 HuEx-1_0-st-v2
> 4033358 HuEx-1_0-st-v2
> 4033362 HuEx-1_0-st-v2
> 3997567 HuEx-1_0-st-v2
> 4033361 HuEx-1_0-st-v2
> 3997576 HuEx-1_0-st-v2
> 8171139 HuGene-1_0-st-v1
> 8177029 HuGene-1_0-st-v1
>
> What do I have to do to find the AGILENT WholeGenome and ILLUMINA HumanWG_6_V2 probes ???
>
> Thank you in advance.
>
>
> ===================================================
> Eduardo Andrés León
> Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 5054)
> e-mail: eandres at cnio.es Fax: (+34) 91 224 69 76
> Unidad de Bioinformática Bioinformatics Unit
> Centro Nacional de Investigaciones Oncológicas
> C.P.: 28029 Zip Code: 28029
> C/. Melchor Fernández Almagro, 3 Madrid (Spain)
> http://bioinfo.cnio.es http://bioinfo.cnio.es/people/eandres
> ===================================================
>
>
>
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Nathan Johnson
Senior Scientific Programmer
Ensembl Regulation
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
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