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

[William Spooner]

Hi Bill,

There are two ways to approach this problem;
1. if you know the actual probe sequences (not the ESTs that the probes were designed against), or can get Applied Microarrays to supply these, you can then use the Ensembl probe mapping pipeline to map these probes to Ensembl genes in the 'approved' manner (genome and cDNA sequence alignment). As you suggest, this may be a touch beyond the call of duty for end users.
2. if you know the EST identifier, you can look this up in the Ensembl database (dna_align_feature), and see what gene(s) overlap(s).

Either way, you will end up with a list of probes vs. Ensembl genes, and you can use the latter for downstream analysis.

All the best,

Will

On 10 May 2011, at 20:08, William Michels wrote:

> 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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--
William Spooner
whs at eaglegenomics.com
http://www.eaglegenomics.com