[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
http://www.ncbi.nlm.nih.gov/gene/?term=17710
and MGI
http://www.informatics.jax.org/marker/MGI:102502
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
Gordon
---------------------------------------------
Professor Gordon K Smyth,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.
http://www.statsci.org/smyth
> sessionInfo()
R version 3.0.1 Patched (2013-07-04 r63183)
Platform: i386-w64-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_Australia.1252
[2] LC_CTYPE=English_Australia.1252
[3] LC_MONETARY=English_Australia.1252
[4] LC_NUMERIC=C
[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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