[BioC] annotation - 1 probe with 2 UG ??

[John Zhang]

>The probeset 220184_at at hgu133a - affymetrix
>is annotated as Hs.479995 if I use the annotation package of BioConductor
>but if I go to netaffx(affymetrix-see details below) is annotated as 
>Hs.329296, in both of them with Symbol: NANOG. Furthermore, using 
>Hs.479995 in affimetrix returns no results.

UniGene clusters change over time. Probe 220184_at was mapped to Hs.479995 in 
the release version but to Hs.329296 in the devel version (which was built 
later). To get the devel version installed you do:

>library(reposTools)
>install.packages2("hgu133a", develOK = TRUE)

>Maybe this is a naive question but shouldn't I suposse that 
>the bioconductor package where created using affymetrix information ?

No. The bioconductor annotation packages were created using various public data 
sources (e. g. LocusLink, GO, KEGG and so on). The information from Affymetrix 
was used to get the unified mappings between probe ids to LocusLink ids only. 

>
>After that I look into NCBI pages and I found that
>Hs.326290 is  NANOG(Nanog homeobox) and Hs.479995  is NANOGP1 
>(Nanog homeobox pseudogene 1) and they both have the same 
>LocusLink identifier and share some GB identifiers
>
>so, is 220184_at a probe with 2 UniGene identifier ?
>
>I appreciate any comment .
>
>Mayte
>
>if you go to netaffx:
>https://www.affymetrix.com/analysis/netaffx/quickquery.affx
>you will find the following annotation:
>---------------------------------------------
>>From Affymetrix:
>220184_at Nanog homeobox NANOG
>regulation of transcription, DNA-dependent
>transcription factor activity
>nucleus
>Probe Set ID   220184_at
>GeneChip Array Human Genome U133 Plus 2.0 Array
>Organism Common Name Human
>Probe Design Information
>Transcript ID g13376297
>Sequence Type Exemplar sequence
>Representative Public ID NM_024865 NCBI
>Archival UniGene Cluster Hs.326290 NCBI
>--------------------------------------------
>
>And using annaffy's functions:  
>
>---------------------------------------------                                                                                                 
>aafUniGene('220184_at','hgu133a')
>An object of class "aafList"
>An object of class "aafUniGene"
>[1] "Hs.479995"
>                                                                                                 
>          Symbol   GenBank LocusLink   UniGene
>220184_at  NANOG NM_024865     79923 Hs.479995
>--------------------------------------------------                                                                                                 
> 
>
>
>Mayte Suarez Farinas
>The Rockefeller University
>1230 York Avenue, Box 212
>New York, NY 10021
>phone: 1-212-327-8186
>fax:   1-212-327-7422
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor

Jianhua Zhang
Department of Biostatistics
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084