[ensembl-dev] Affymetrix Porcine probes: genomic position

[Nathan Johnson]

Hi Dario

The annotation from the transcript mapping (probe2transcript) process may help here. Firstly, our probe/set annotations are generated at the transcript level. So this may give you an insight to the differential expression you may be seeing. Also, for any given probeset-transcript xref, using the API you can retrieve which probe mappings were considered i.e. passed our xref rules (defined here http://www.ensembl.org/info/docs/microarray_probe_set_mapping.html).

These individual probe mapping transcript xrefs are stored as DBEntries for the ProbeFeature in question, look in the linkage_annotation for more info about the mapping. Probes/Sets which are considered for an xref transcript but fail are stored as UnmappedObjects, look in the summary or description for more info about the failure. 

The example script I pointed you towards should contain all the code to retrieve this info.


Nath


On 26 Apr 2011, at 15:00, Dario Beraldi wrote:

> Ok, thanks Nath.
> 
> (Just for information, I found that sometimes probes mapping to the same gene show quite discordant expression patterns. So I wanted to get the probe position to see if this discrepancy could be explained by differential splicing or other biological event or it is just the result of technical artifacts.)
> 
> Best wishes
> Dario
> 
> 
> Quoting Nathan Johnson <njohnson at ebi.ac.uk> on Tue, 26 Apr 2011 14:18:06 +0100:
> 
>> Hi Dario
>> 
>> We do store array data in the Ensembl Biomart, but this is restricted to the transcript annotations based on the various arrays we cater for, including the Affy porcine array. This is present in the gene mart as an 'External' attribute, but we do not store individual mappings here, just probe/probe_set annotations.
>> 
>> We don't currently provide genome wide array/probe mappings as dumps, primarily because we have had little to no demand for this.
>> 
>> It would be possible to create these using the API. There is an example script available here which should give you the necessary methods:
>> 
>> 	ensembl-functgenomics/scripts/examples/microarray_annotation_example.pl
>> 
>> 
>> Thanks
>> 
>> Nath
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> On 26 Apr 2011, at 13:55, Dario Beraldi wrote:
>> 
>>> Hi Laurent,
>>> 
>>> Thanks for taking time to reply. Unfortunately, the file Sus_scrofa.gvf.gz has the probe location for the Illumina Porcine SNP chip. What I'm after is the probe location of the Affymetrix Porcine gene expression array (this one: http://www.affymetrix.com/browse/products.jsp?productId=131488&navMode=34000&navAction=jump&aId=productsNav#1_1).
>>> 
>>> I had a look into the subdirectories within ftp://ftp.ensembl.org/pub/release-62/ I but couldn't find anything relevant.
>>> 
>>> Any ideas...?
>>> 
>>> All the best
>>> Dario
>>> 
>>> Quoting Laurent Gil <lgil at ebi.ac.uk> on Tue, 26 Apr 2011 13:27:33 +0100:
>>> 
>>>> Hi Dario,
>>>> 
>>>> You can find all the ensembl data on the ftp: http://www.ensembl.org/info/data/ftp/index.html
>>>> 
>>>> The pig variations are stored here: ftp://ftp.ensembl.org/pub/release-62/variation/sus_scrofa/
>>>> The file that might interest you is Sus_scrofa.gvf.gz <ftp://ftp.ensembl.org/pub/release-62/variation/sus_scrofa/Sus_scrofa.gvf.gz>.
>>>> 
>>>> Cheers,
>>>> 
>>>> Laurent
>>>> 
>>>> 
>>>> On 25/04/2011 19:23, Dario Beraldi wrote:
>>>>> Hello,
>>>>> 
>>>>> I'm working with the Affymetrix Porcine chip (gene expression array for pig). I would like to download the position where each probe maps on the pig genome.
>>>>> 
>>>>> (I can see this information is present somewhere in ENSEMBL for example http://www.ensembl.org/Sus_scrofa/Location/Genome?db=core;fdb=funcgen;ftype=ProbeFeature;g=ENSSSCG00000014369;id=Ssc.4978.1.S1_at;ptype=pset;r=2:129356198-129357848;t=ENSSSCT00000015699 but I can't figure out how to extract the genome position in batch for all the probes).
>>>>> 
>>>>> Many thanks!
>>>>> 
>>>>> Dario
>>>>> 
>>>> 
>>> 
>>> 
>>> 
>>> --
>>> 
>>> Dr. Dario Beraldi
>>> Institute of Evolutionary Biology
>>> University of Edinburgh
>>> West Mains Road
>>> Edinburgh EH9 3JT
>>> Scotland, UK
>>> 
>>> 
>>> --
>>> The University of Edinburgh is a charitable body, registered in
>>> Scotland, with registration number SC005336.
>>> 
>>> 
>>> 
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>> 
>> Nathan Johnson
>> Senior Scientific Programmer
>> Ensembl Regulation
>> European Bioinformatics Institute
>> Wellcome Trust Genome Campus
>> Hinxton
>> Cambridge CB10 1SD
>> 
>> http://www.ensembl.info/
>> http://twitter.com/#!/ensembl
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
> 
> 
> 
> -- 
> 
> Dr. Dario Beraldi
> Institute of Evolutionary Biology
> University of Edinburgh
> West Mains Road
> Edinburgh EH9 3JT
> Scotland, UK
> 
> 
> -- 
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
> 

Nathan Johnson
Senior Scientific Programmer
Ensembl Regulation
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD

http://www.ensembl.info/
http://twitter.com/#!/ensembl