[BiO BB] expression level by EST by family

Harry Mangalam harry.mangalam at uci.edu
Fri Mar 7 14:07:32 EST 2008


(apologies if this posted 2x - possible mail burp)

Posting for a colleague:

<post>
I'm looking for tools to do a little data mining in the NCBI data 
base. Specifically what I'm interested in is obtaining the EST 
frequency as a measure of the expression levels of members of a 
particular gene family (Na/K ATPases) by organism (mouse) and tissue 
type (heart). I've browsed the EST database and it looks like the 
data is in there but what I need is a tool that can search all 
records in each relevant data base. Any ideas or pointers in the 
right direction?
</post>

It sounds like what he needs is an SQL-like interface to dbEST; is 
there such a thing extant or is this something that will have to be 
writ using a bio* toolkit to NCBI's or other API?

It does look like Ensembl's Biomart could answer questions like this 
tho - can anyone confirm?
-- 
Harry Mangalam - Research Computing, NACS, E2148, Engineering Gateway, 
UC Irvine 92697  949 824 0084(o), 949 285 4487(c)
--
[A Nation of Sheep breeds a Government of Wolves.
Edward R. Murrow]




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