[BioC] org.Mm.eg.db gives wrong symbol for MT genes

Gordon K Smyth smyth at wehi.EDU.AU
Sat Aug 10 05:17:03 CEST 2013

Dear Biocore,

We make a strong effort to use current NCBI official gene symbols and 
names in all our work, and we make much use of the excellent Bioconductor 
packages org.Mm.eg.db and org.Hs.eg.db for this purpose.

I have recently noticed that org.Mm.eg.db is giving incorrect official 
names for mitochondrial genes.  It is giving human symbols for these genes 
instead of mouse symbols.  For example

   > mappedRkeys(org.Mm.egSYMBOL["17710"])
   [1] "COX3"

According to both Entrez Gene


and MGI


the official symbol is "mt-Co3".  This has been the official symbol for at 
least 4 years and probably longer.

The correct name is not even included as an Alias:

   > mappedRkeys(revmap(org.Mm.egALIAS2EG)["17710"])
   [1] "COX3"

COX3 is the actually the symbol for the human ortholog.  It should only be 
an alias for the mouse gene.

Same for all the mitochondrial genes.  In all cases, org.Mm.egSYMBOL is 
giving the human symbol instead of the mouse symbol.

Is this deliberate?  If not, can you please fix?

Thanks a lot

Professor Gordon K Smyth,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.

> sessionInfo()
R version 3.0.1 Patched (2013-07-04 r63183)
Platform: i386-w64-mingw32/i386 (32-bit)

[1] LC_COLLATE=English_Australia.1252
[2] LC_CTYPE=English_Australia.1252
[3] LC_MONETARY=English_Australia.1252
[5] LC_TIME=English_Australia.1252

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets
[7] methods   base

other attached packages:
[1] org.Mm.eg.db_2.9.0   org.Hs.eg.db_2.9.0   RSQLite_0.11.4
[4] DBI_0.2-7            AnnotationDbi_1.22.6 Biobase_2.20.0
[7] BiocGenerics_0.6.0   limma_3.17.20

loaded via a namespace (and not attached):
[1] IRanges_1.18.2 stats4_3.0.1

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