[Arabidopsis] Re: good set of "housekeeping" genes in AT?
(by evewurtele from gmail.com)
Sat Oct 3 18:30:38 EST 2009
If you are concerned with more than developmental expression, 100 genes that
vary least across about 1000 Affy chips (500 samples) from AtGenExpress are
described in Mentzen 2008. (The chips include the developmental series, plus
a variety of environmental and genetic perturbations). The reference as
well as the actual "steady" gene list are below. BMC Plant Biol. 2008 Sep
30;8:99. Regulon organization of
Listed at supplementary "*Additional file 5.* Genes with the most steady
Two quite steady transcripts with a high overall level of accumulation are :
AT3G56460 and AT4G34110 (These transcripts have about 5-fold and 7-fold,
respectively, higher accumulation than the mean value of the genes on the
chips, which is set to 100)
The genes with most steady expression comprise a fairly uniform mixture of
metabolism, regulation, transport, and "unknown" functions.
However, no "steady" "housekeeping" genes on the affy chip are completely
steady. Thus, it makes sense to be sure the particular conditions you are
testing (say "heat stress") are not the ones under which the "housekeeping
gene" varies. For each gene, there are a couple conditions/in a couple chips
out of the 500 in which there is variation (say 2-fold greater or less than
the mean). You can use
the conditions where there is a bit more variation. Download
(free- funded by NSF-Arabidopsis 2010), a window will open. download
Affy.ath1.data1 project, clicking the blue +to create a new gene list, and
paste the locus IDs shown below into a the gene list after clicking import.
(that's what I did to get the particular three genes listed above, its quick
once you've learned the software)
*Locus ID- Most steady expression- Mentzen and Wurtele, BMC Plant Biology
> On Fri, Oct 2, 2009 at 4:05 AM, Neil Graham <neil from arabidopsis.info> wrote:
>> Have a look at:
>> Czechowsli et al 2005. Genome-wide identification of superior reference
>> genes for transcript normalisation in Arabidopsis. Plant Physiology.
>> These genes were identified by finding genes with a low %CV across the
>> AtGenExpress developmental series.
>> Neil Graham
>> Nottingham Arabidopsis Stock Centre
>> Plant and Crop Sciences Division
>> University of Nottingham
>> Karen Browning wrote:
>>> What would be a good set of housekeeping genes to use for "standards" for
>>> comparing expression data in Arabidopsis?
>>> Anyone have a standard list of At gene numbers that they use, e.g. actin,
>>> tubulin, etc.?
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> Eve Syrkin Wurtele, Professor
> Bioinformatics and Computational Biology
> 2624D Howe Hall, VRAC,
> Iowa State University, Ames IA 50011, USA
> metablast.org 515-708-3232 (cell)
Eve Syrkin Wurtele, Professor
Bioinformatics and Computational Biology
2624D Howe Hall, VRAC,
Iowa State University, Ames IA 50011, USA
metablast.org 515-708-3232 (cell)
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