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

William Michels michelsw at anesthesia.ucsf.edu
Wed May 11 20:15:59 BST 2011

Hi Will,

Thanks for the note. The problem looks very serious from my  
perspective. Here's what I found in BioMart:  only 4922 / 29516 rat  
genes with Codelink IDs.

Dataset 4922 / 29516 Genes

Rattus norvegicus genes (RGSC3.4)
[None selected]
with Codelink ID(s): Only
Ensembl Gene ID
Ensembl Transcript ID
Associated Gene Name

On May 10, 2011, at 12:53 PM, William Spooner wrote:

> 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

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