AW: [Arabidopsis] Re: good set of "housekeeping" genes in AT?

Wolf-Ruediger Scheible via arab-gen%40net.bio.net (by Scheible from mpimp-golm.mpg.de)
Mon Oct 5 01:11:23 EST 2009



For clarification: the paper by Czechowski et al. (2005) identified novel reference genes not just from the AtGE developmental series but also from

- a large abiotic stress series
- hormone treatments
- a biotic stress treatments
- nutrient stress/re-addition experiments
and a diurnal series

The genes we finally proposed performed well in all these experimental conditions.

Regards, Wolf

Dr. Wolf Scheible
Max-Planck Institute of Molecular Plant Physiology
Science Park Golm 
Am Mühlenberg 1
14476 Potsdam, Germany

phone +49-331-5678155
fax +49-331-5678134

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Von: arab-gen-bounces from oat.bio.indiana.edu [mailto:arab-gen-bounces from oat.bio.indiana.edu] Im Auftrag von Eve Wurtele
Gesendet: Sunday, October 04, 2009 1:31 AM
An: bionet-genome-arabidopsis from moderators.isc.org
Betreff: Re: [Arabidopsis] Re: good set of "housekeeping" genes in AT?

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 Arabidopsis.<http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18826618>
*Mentzen WI*<http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18826618>,
<http://goog_1254598750316>*Wurtele
ES*<http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18826618>.
Listed at supplementary "*Additional file 5.* Genes with the most steady expression"<http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18826618>
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 MetaOmGraph<http://metnetdb.org/MetNet_MetaOmGraph.htm>to visualize 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)


> On Fri, Oct 2, 2009 at 4:05 AM, Neil Graham <neil from arabidopsis.info> wrote:
>
>> Hi
>>
>> Have a look at:
>>
>> Czechowsli et al 2005. Genome-wide identification of superior 
>> reference genes for transcript normalisation in Arabidopsis. Plant Physiology.
>> 139:5-17.
>>
>> These genes were identified by finding genes with a low %CV across 
>> the AtGenExpress developmental series.
>>
>> Thanks
>>
>> Neil Graham
>>
>> --------------------------------------
>> http://arabidopsis.info
>>
>> Nottingham Arabidopsis Stock Centre
>> Plant and Crop Sciences Division
>> University of Nottingham
>> Loughborough
>> UK
>> --------------------------------------
>>
>> 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 metnetdb.org
> 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 metnetdb.org
metablast.org                      515-708-3232 (cell)
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