how to find the list of probe sets in Affy U133A that correspond to housekeeping genes
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@james-anderson-1641
Last seen 7.2 years ago
Hi, I am trying to find a list of probe sets in Affy U133A that correspond to housekeeping genes to perform some normalization, where can I find that list? Thanks, -James [[alternative HTML version deleted]]
Normalization probe affy Normalization probe affy • 947 views
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 5.3 years ago
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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. But do you really need an official list if you have a good sized data set? Perhaps you only need to just find genes that do not vary much across your dataset. Maybe you might want to look at the varFilter function in the geneFilter package? library("genefilter") ?varFilter Hope this helps, Marc On 04/13/2010 01:13 PM, James Anderson wrote: > Hi, > > I am trying to find a list of probe sets in Affy U133A that correspond to housekeeping genes to perform some normalization, where can I find that list? > > Thanks, > > -James > > > > [[alternative HTML version deleted]] > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
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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.1000 598 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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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@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.1000 598 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 _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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