annotation for TAqman assay IDs
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@bernard-north-6674
Last seen 7.7 years ago
I have a list of Taqman assay IDs that I am trying to annotate eg MSMB-Hs00159303_m1. They are all exon-spanning probe assays (ie ending _m1) as described here http://www.lifetechnologies.com/uk/en/home /communities-social/blog/blogs/the-hows-whats-and-whys-of-gene- expression-assay-design.html The Life Technologies website does provides some information for each assay at https://www.lifetechnologies.com/us/en/home/life-science/pcr /real-time-pcr/real-time-pcr-assays.html. After searching for gene expression assays for MSMB and clicking on "gene expression" a list of assays appears eg Hs00159303_m1 and when I click on "view details" I'm able to discover the Entrez ID is 4477, the UniGene ID is Hs.255462, as well as other useful information. I wondered if there was any automatic way via a bioconductor function of obtaining such useful annotation of Taqman assay IDs. Often the part of the assay name before the -Hs seems to be the HUGO gene symbol (so that lends itself to BIoMart) but that's not always the case eg NKX3-1-Hs00171834_m1 (NKX3-1 is not a HUGO symbol). Many thanks in advance [[alternative HTML version deleted]]
Annotation probe annotate Annotation probe annotate • 1.3k views
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@james-w-macdonald-5106
Last seen 15 hours ago
United States
Hi Bernard, On 7/29/2014 11:46 AM, Bernard North wrote: > I have a list of Taqman assay IDs that I am trying to annotate eg MSMB-Hs00159303_m1. They are all exon-spanning probe assays (ie ending _m1) as described here http://www.lifetechnologies.com/uk/en/home /communities-social/blog/blogs/the-hows-whats-and-whys-of-gene- expression-assay-design.html > > The Life Technologies website does provides some information for each assay at https://www.lifetechnologies.com/us/en/home/life- science/pcr/real-time-pcr/real-time-pcr-assays.html. After searching for gene expression assays for MSMB and clicking on "gene expression" a list of assays appears eg Hs00159303_m1 and when I click on "view details" I'm able to discover the Entrez ID is 4477, the UniGene ID is Hs.255462, as well as other useful information. > I wondered if there was any automatic way via a bioconductor function of obtaining such useful annotation of Taqman assay IDs. Often the part of the assay name before the -Hs seems to be the HUGO gene symbol (so that lends itself to BIoMart) but that's not always the case eg NKX3-1-Hs00171834_m1 (NKX3-1 is not a HUGO symbol). > It appears that they are appending the HUGO symbol, as NKX3-1 is a HUGO symbol: http://www.genenames.org/cgi- bin/gene_symbol_report?q=data/hgnc_data.php&hgnc_id=7838 You could use either biomaRt or the org.Hs.eg.db packages to annotate using the gene symbols. > select(org.Hs.eg.db, c("NKX3-1","MSMB"), c("ENTREZID","SYMBOL","GENENAME"), "ALIAS") ALIAS ENTREZID SYMBOL GENENAME 1 NKX3-1 4824 NKX3-1 NK3 homeobox 1 2 MSMB 4477 MSMB microseminoprotein, beta- But using symbols is not guaranteed to get you 100% accurate mappings, so caveat emptor. Best, Jim > Many thanks in advance > > > [[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
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