[BioC] annotation for TAqman assay IDs

[James W. MacDonald]

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
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099