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-   -   mRNA expression level data base (http://seqanswers.com/forums/showthread.php?t=21928)

blueStone 07-23-2012 10:06 AM

mRNA expression level data base
 
Hello everyone,

I am looking for a database in which to find mRNA expression levels for corresponding sequences. Being new to this site, I might be in the wrong subforum and I am definately a user and not a developer, so please bear with my blunt question, but if anybody could point me towards such a database that would be so great!

Background: I would like to make an educated guess as to what degree given oligonucleotide-like probes would interact with a given genome in a given tissue. My thought here was to check the sequences for matches with edit distance 0, 1 and 2 against the given genome. But then it occured to me, that besides hard-coded repeats in the DNA, some mRNA might exist in a tissue also in thousands of copies. So, now I have to weight (imperfect) matches with frequencies ... for which I would need the above mentioned mRNA-expression database.

If there is a simpler or more elegant approach, please let me know as well,
thank you for your help,

Matthias

simonandrews 07-24-2012 12:13 AM

The resource we use for this kind of thing is BioGPS. This works on a large dataset of expression array data across a big tissue panel. Given that your question is about the level of oligo association in different tissues it's probably the closest thing you're going to get.

Wolfgang Huber 07-29-2012 10:42 AM

Dear Matthias
have a look at ArrayExpress, in particular their Gene Expression Atlas.
Best wishes
Wolfgang


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