Gene Synonym
An r package that works as a wrapper to synonym information in ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz. Updates semi-regularly since 8th of Match 2017
Available species are
geneSynonym::taxData## tax_id name_txt
## 1 10090 Mus musculus
## 2 10116 Rattus norvegicus
## 3 28985 Kluyveromyces lactis
## 4 318829 Magnaporthe oryzae
## 5 33169 Eremothecium gossypii
## 6 3702 Arabidopsis thaliana
## 7 4530 Oryza sativa
## 8 4896 Schizosaccharomyces pombe
## 9 4932 Saccharomyces cerevisiae
## 10 5141 Neurospora crassa
## 11 6239 Caenorhabditis elegans
## 12 7165 Anopheles gambiae
## 13 7227 Drosophila melanogaster
## 14 7955 Danio rerio
## 15 8364 Xenopus (Silurana) tropicalis
## 16 9031 Gallus gallus
## 17 9544 Macaca mulatta
## 18 9598 Pan troglodytes
## 19 9606 Homo sapiens
## 20 9615 Canis lupus familiaris
## 21 9913 Bos taurus
## 22 562 Escherichia coli
More species can be added on request
Installation
library(devtools)
install_github('oganm/geneSynonym')Usage
The output is a nested list since gene synonyms are not nececarilly unique. For instance
mouseSyno('Tex40')## $Tex40
## $Tex40$`16528`
## [1] "Kcnk4" "Catsperz" "MLZ-622" "TRAAK" "TRAAKt" "Tex40"
##
## $Tex40$`67077`
## [1] "Catsperz" "1700019N12Rik" "A430107B04Rik" "MLZ-622"
## [5] "Tex40"
Names of vectors within the list are NCBI ids.
Input is a vector of gene names/NCBI ids and a tax identifier. Alternatively shorthand functions exist for human and mouse.
geneSynonym(c('Eno2','Mog'), tax = 10090)## $Eno2
## $Eno2$`13807`
## [1] "Eno2" "D6Ertd375e" "Eno-2" "NSE"
##
##
## $Mog
## $Mog$`17441`
## [1] "Mog" "B230317G11Rik"
geneSynonym(c('Eno2','Mog'), tax = 10090)## $Eno2
## $Eno2$`13807`
## [1] "Eno2" "D6Ertd375e" "Eno-2" "NSE"
##
##
## $Mog
## $Mog$`17441`
## [1] "Mog" "B230317G11Rik"
mouseSyno(c('Eno2',17441))## $Eno2
## $Eno2$`13807`
## [1] "Eno2" "D6Ertd375e" "Eno-2" "NSE"
##
##
## $`17441`
## $`17441`$`17441`
## [1] "Mog" "B230317G11Rik"
humanSyno('MOG')## $MOG
## $MOG$`4340`
## [1] "MOG" "BTN6" "BTNL11" "MOGIG2" "NRCLP7"