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Question: where to find a list of housekeeping genes for Affy array (Gene 1.0 ST)
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gravatar for Jack Luo
4.6 years ago by
Jack Luo340
Jack Luo340 wrote:
Not sure whether it's an appropriate question for Bioconductor. Is there a place to find a list of housekeeping genes (identified by Affy)? Thanks, -Jack [[alternative HTML version deleted]]
ADD COMMENTlink modified 4.6 years ago by Robert Castelo2.0k • written 4.6 years ago by Jack Luo340
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gravatar for shirley zhang
4.6 years ago by
shirley zhang1.0k
shirley zhang1.0k wrote:
Hi Jack, You can find housekeeping transcripts defined based on previous analysis of 18 human tissues. You can download a list of ~2,000 housekeeping genes by following the link in below paper. Zhu J, He F, Song S, Wang J, Yu J. How many human genes can be defined as housekeeping with current expression data? BMC Genomics 2008;9:172. Shirley On Wed, Apr 17, 2013 at 8:03 PM, Jack Luo <jluo.rhelp at="" gmail.com=""> wrote: > Not sure whether it's an appropriate question for Bioconductor. Is there a > place to find a list of housekeeping genes (identified by Affy)? > > Thanks, > > -Jack > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 4.6 years ago by shirley zhang1.0k
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gravatar for Robert Castelo
4.6 years ago by
Robert Castelo2.0k
Spain/Barcelona/Universitat Pompeu Fabra
Robert Castelo2.0k wrote:
hi, if you're searching from something readily available in R, you can try to do following: library(BiocInstaller) ## assuming you installed some BioC package once biocLite("tweeDEseqCountData") library(tweeDEseqCountData) data(hkGenes) length(hkGenes) [1] 669 head(hkGenes) [1] "ENSG00000149925" "ENSG00000102144" "ENSG00000142676" "ENSG00000108298" [5] "ENSG00000144713" "ENSG00000075624" check out the help page of 'hkGenes' for the source publication of this list. as you see, these are Ensmbl gene identifiers, but if you need Affy IDs from a particular Affy chip, let's say HG-U133 Plus 2.0, you can use the great identifier mapping functionality of the package GSEABase, which in principle is designed to map identifier between gene sets and ExpressionSet objects, but which you can tweak to do this job for you passing the housekeeping gene list as if it were one gene set: library(GSEABase) dummygs <- GeneSet(hkGenes, geneIdType=ENSEMBLIdentifier()) hkGenesHGU133plus2AffyIDs <- geneIds(mapIdentifiers(dummygs, AnnoOrEntrezIdentifier("hgu133plus2"))) length(hkGenesHGU133plus2AffyIDs) [1] 1263 head(hkGenesHGU133plus2AffyIDs) [1] "200966_x_at" "214687_x_at" "238996_x_at" "1558365_at" "200737_at" [6] "200738_s_at" cheers, robert. On 04/18/2013 02:03 AM, Jack Luo wrote: > Not sure whether it's an appropriate question for Bioconductor. Is there a > place to find a list of housekeeping genes (identified by Affy)? > > Thanks, > > -Jack > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Robert Castelo, PhD Associate Professor Dept. of Experimental and Health Sciences Universitat Pompeu Fabra (UPF) Barcelona Biomedical Research Park (PRBB) Dr Aiguader 88 E-08003 Barcelona, Spain telf: +34.933.160.514 fax: +34.933.160.550
ADD COMMENTlink written 4.6 years ago by Robert Castelo2.0k
On 4/19/2013 9:25 AM, Robert Castelo wrote: > hi, > > if you're searching from something readily available in R, you can try > to do following: > > library(BiocInstaller) ## assuming you installed some BioC package once > biocLite("tweeDEseqCountData") > > library(tweeDEseqCountData) > data(hkGenes) > length(hkGenes) > [1] 669 > head(hkGenes) > [1] "ENSG00000149925" "ENSG00000102144" "ENSG00000142676" > "ENSG00000108298" > [5] "ENSG00000144713" "ENSG00000075624" > > check out the help page of 'hkGenes' for the source publication of > this list. > > as you see, these are Ensmbl gene identifiers, but if you need Affy > IDs from a particular Affy chip, let's say HG-U133 Plus 2.0, you can > use the great identifier mapping functionality of the package > GSEABase, which in principle is designed to map identifier between > gene sets and ExpressionSet objects, but which you can tweak to do > this job for you passing the housekeeping gene list as if it were one > gene set: > > library(GSEABase) > > dummygs <- GeneSet(hkGenes, geneIdType=ENSEMBLIdentifier()) > > hkGenesHGU133plus2AffyIDs <- geneIds(mapIdentifiers(dummygs, > AnnoOrEntrezIdentifier("hgu133plus2"))) > > length(hkGenesHGU133plus2AffyIDs) > [1] 1263 > > head(hkGenesHGU133plus2AffyIDs) > [1] "200966_x_at" "214687_x_at" "238996_x_at" "1558365_at" "200737_at" > [6] "200738_s_at" Or you could use more direct methods: library(hgu133plus2.db) mapped.genes <- select(hgu133plus2.db, hkGenes, "PROBEID", "ENSEMBL") head(mapped.genes) ENSEMBL PROBEID 1 ENSG00000149925 200966_x_at 2 ENSG00000149925 214687_x_at 3 ENSG00000149925 238996_x_at 4 ENSG00000102144 1558365_at 5 ENSG00000102144 200737_at 6 ENSG00000102144 200738_s_at Best, Jim > > > cheers, > robert. > > > On 04/18/2013 02:03 AM, Jack Luo wrote: >> Not sure whether it's an appropriate question for Bioconductor. Is >> there a >> place to find a list of housekeeping genes (identified by Affy)? >> >> Thanks, >> >> -Jack >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD REPLYlink written 4.6 years ago by James W. MacDonald45k
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