[BioC] how to find the list of probe sets in Affy U133A that correspond to housekeeping genes

[Steve Lianoglou]

Hi,

On Wed, Apr 14, 2010 at 3:41 PM, Marc Carlson <mcarlson at fhcrc.org> wrote:
> AFAIK, there is not an official list of housekeeping genes anywhere.  I
> know that some genes are popular to use for this purpose (ubiquitin for
> example) but I don't think there is an official list anywhere.  If there
> is one, I would love to know about it.

Also, the definition of what a "housekeeping" gene really is makes you
wonder after reading this paper:

An Abundance of Ubiquitously Expressed Genes Revealed by Tissue
Transcriptome Sequence Data
http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000598

They peg the number of ubiquitously expressed genes to be ~ 8k (I
think they surveyed ~ 25 rna-seq expts from different cell
types/lines).

So, where do we draw the line between a housekeeping gene and a
ubiquitously expressed one? Is there one, and how do we find it?

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact