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

Eve Wurtele via arab-gen%40net.bio.net (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
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)

*Locus ID- Most steady expression- Mentzen and Wurtele, BMC Plant Biology
2008*
AT5G12370
AT4G15415
AT4G15475
AT4G17430
AT1G73440
AT5G11040
AT5G28850; AT5G28900
AT5G21040
AT4G37130
AT3G56830
AT1G16570
AT5G16280
AT5G24830
AT5G65540
AT5G64830
AT5G64813
AT5G61840
AT5G48520
AT5G46190
AT5G45300
AT5G41480
AT5G38380
AT5G38360
AT5G37310
AT5G24360
AT5G18190
AT5G11490
AT5G11640
AT5G11380
AT5G07270
AT5G05920
AT5G05820
AT5G04070
AT5G02850
AT3G56460
AT3G55480
AT3G53090
AT3G52610
AT3G51040
AT3G51050
AT3G49850
AT3G47390
AT3G42050
AT4G39920
AT4G38040
AT4G38500
AT4G38180
AT4G35530
AT4G34110
AT4G31150
AT4G26410
AT4G11970
AT4G00420
AT3G28670
AT3G27320
AT3G17430
AT3G17450
AT1G53770
AT3G17750
AT3G20870
AT3G29010
AT3G04470
AT3G05040
AT3G04970
AT3G33520
AT3G05090; AT3G05080
AT1G13320
AT1G68980
AT1G73840
AT1G73970
AT1G34550
AT1G79810
AT1G01910
AT1G76340
AT1G80950
AT1G79975
AT1G54390
AT1G54150
AT1G05500
AT2G40410
AT2G36240
AT1G78810
AT1G08960
AT1G08750
AT2G17390
AT1G76940
AT1G30970
AT2G28390
AT2G38950
AT2G27600
AT2G27110
AT2G41350
AT2G35100
AT2G35360
AT2G40980
AT2G19280
AT2G39910
AT2G41960


> 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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