[ensembl-dev] Affymetrix Porcine probes: genomic position

[Dario Beraldi]

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.