[ensembl-dev] probe mapping for transcripts

Fri Jun 17 11:44:25 BST 2011

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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