[ensembl-dev] Codelink probe list...incomplete?

[William Michels]

Hi Ensembl people,

We've recently begun using the "Codelink" microarray platform to  
analyze whole genome gene expression in rat. This product was  
developed by Amersham/GE_Healthcare, and is still being manufactured  
to this day by a spin-off company named Applied Microarrays (Tempe,  
AZ, USA). I have no affiliation with the company. The Rat Whole  
Genome platform file is GPL2896. We chose this platform as a 'first  
pass' to check gene expression levels relative to certain treatment  
regimes, with an eye towards KEGG or GO style pathway analysis.

Because of the age of the chipset relative to the Rat Genome  
sequencing efforts at the time (~2005), many thousands of the probes  
were solely identified by EST identifiers. Now many years later,  
thousands of the probes are still solely identified by EST identifiers.

My question is whether there is an Ensembl effort underway to update  
these whole-genome platform files (human, mouse, rat), specifically  
GPL2896??? The computational resources required to BLAST identify  
unknown genes for tens of thousands of EST sequences seems far beyond  
the capabilities of a simple end user. Furthermore the lack of a full  
per-gene information record ('hole-y data') makes it very difficult  
if not impossible to do pathway analysis.

Any advice appreciated,

Best Regards, Bill.

William Michels, Ph.D.
Assistant Research Biochemist
Department of Anesthesia
University of California, San Francisco
513 Parnassus Avenue  S-261, Box 0542
San Francisco, CA 94143
phone: (415) 476-6231
fax (415) 476-8841
email: michelsw at anesthesia.ucsf.edu




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