Dear Bioconductor,
I find fewer genes for a given GO term in mouse with the org.Mm.eg.db
than with teh online AMIGO server. I am wondering if the difference is
due to delays in updating org.Mm.eg.db, or for some other reason.
Here is my R session
library(AnnotationDbi)
> library(org.Mm.eg.db)
> GO0044339.ids<-select(org.Mm.eg.db,keys="GO:0044339",columns=c("GO","ENTREZID","SYMBOL"),keytype="GO")
'select()' returned 1:many mapping between keys and columns
> GO0044339.ids
GO EVIDENCE ONTOLOGY ENTREZID SYMBOL
1 GO:0044339 ISO BP 14362 Fzd1
2 GO:0044339 ISO BP 22415 Wnt3
3 GO:0044339 IMP BP 100201 Tmem64
> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.6
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] org.Mm.eg.db_3.4.0 GO.db_3.4.0 AnnotationDbi_1.36.2 IRanges_2.8.2 S4Vectors_0.12.2
[6] Biobase_2.34.0 BiocGenerics_0.20.0
loaded via a namespace (and not attached):
[1] tools_3.3.3 DBI_0.6-1 memoise_1.1.0 Rcpp_0.12.11 RSQLite_1.1-2 digest_0.6.12
>
Here is the result of my Amigo search
Search term:
GO:0044339
organosm: mouse
MGI:MGI:2665790 Tnn
MGI:MGI:2140359 Tmem64
MGI:MGI:1196625 Fzd1
MGI:MGI:98955 Wnt3
There is one additional gene: Tnn
Is this discrepancy due to a delay in updating org.Mm.eg.db,
or some other reason?
I also get the same 4 genes with annotations search in mmigo as I fo with gene products
MGI MGI:2665790 Tnn GO:1905240 MGI:MGI:3710297|PMID:17395156 IDA P tenascin N tenascin-W|Tnw protein NCBITaxon:10090 20170210 UniProt
MGI MGI:2140359 Tmem64 GO:0044339 MGI:MGI:5643786|PMID:25979161 IMP P transmembrane protein 64 9630015D15Rik protein NCBITaxon:10090 20160212 UniProt
MGI MGI:1196625 Fzd1 GO:0044339 MGI:MGI:4834177|GO_REF:0000096 ISO UniProtKB:Q9UP38 P frizzled class receptor 1 Fz1|FZ-1 protein NCBITaxon:10090 20100930 MGI
MGI MGI:98955 Wnt3 GO:0044339 MGI:MGI:4834177|GO_REF:0000096 ISO UniProtKB:P56703 P wingless-type MMTV integration site family, member 3 Int-4|Wnt-3 protein NCBITaxon:10090 20100930 MGI
Thanks and best wishes,
Rich
Richard A. Friedman, PhD
Associate Research Scientist,
Biomedical Informatics Shared Resource
Herbert Irving Comprehensive Cancer Center (HICCC)
Lecturer,
Department of Biomedical Informatics (DBMI)
Room 825
Irving Cancer Research Center
Columbia University Herbert and Florence Irving Medical Center
1130 St. Nicholas Ave
New York, NY 10032
(212)851-4765 (voice)
raf4@cumc.columbia.edu
http://www.columbia.edu/~raf4/index.html
“Will there still be "Classics Illustrated” by the time I have children? I cannot
imagine raising kids without "Classics Illustrated” .” -Rose Friedman, age 20
Jim,
Thank you, as always but I still am not getting all the genes (I am still on R 3.3.3 because there is an intermittent problem with
permissions on my mac which I want to solve before I update. Should that make a difference).
> select(org.Mm.eg.db,keys="GO:0044339",column="SYMBOL",keytype="GOALL")
'select()' returned 1:many mapping between keys and columns
GOALL EVIDENCEALL ONTOLOGYALL SYMBOL
1 GO:0044339 ISO BP Fzd1
2 GO:0044339 ISO BP Wnt3
3 GO:0044339 IMP BP Tmem64
> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.6
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] org.Mm.eg.db_3.4.0 AnnotationDbi_1.36.2 IRanges_2.8.2 S4Vectors_0.12.2 Biobase_2.34.0
[6] BiocGenerics_0.20.0
loaded via a namespace (and not attached):
[1] tools_3.3.3 DBI_0.6-1 memoise_1.1.0 Rcpp_0.12.11 RSQLite_1.1-2 digest_0.6.12
>
I too am still getting used to Rose as a grownup.
Thank you as always,
Rich
When you go to the AmiGO website you get the most current mappings, whereas the OrgDb packages for a given Bioconductor release are frozen as of a couple weeks before the release. So the data you have in hand are from over a year ago (you have Bioc-3.4, which was released in October last year, so that org.Mm.eg.db package was current as of late September/early October 2016).
It's quite likely that there are numerous other changes that have occurred in the intervening period as well. Unfortunately, if you don't keep your R/Bioc installation updated, you fall behind on the annotation data.