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

[Christos Hatzis]

One can get a reasonable answer on what housekeeping genes are only if the
"invariance" of these genes is defined more clearly.  For example, one can
consider genes like actin or GAPDH as relatively invariant genes for normal
cells as the encode for proteins needed for basic functions, which should be
similarly expressed for most normally proliferating genes.  However, how
these genes might be expressed in a highly proliferative tumor cell, that's
a totally different story.  So it would not be such a great idea to use the
levels of these genes to normalize expression values between a set of normal
samples and a set of tumor samples, if that was the intention.

The "invariance" aspect of the normalizing (better term than housekeeping if
they are to be used for normalizing) genes is related to the application at
hand.  Once this is defined somehow, invariant genes can be selected based,
for example, on invariant ranks between the two or more sets of samples that
need to be jointly normalized.

-Christos

Christos Hatzis, Ph.D.
Nuvera Biosciences, Inc.
400 West Cummings Park, Suite 5350
Woburn, MA 01801
781-938-3844   

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Steve Lianoglou
Sent: Wednesday, April 14, 2010 4:04 PM
To: Marc Carlson
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] how to find the list of probe sets in Affy U133A that
correspond to housekeeping genes

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

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