An r package that works as a wrapper to synonym information inftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz. Updatessemi-regularly since 8th of Match 2017
Available species are
## 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
library(devtools)install_github('oganm/geneSynonym')The output is a nested list since gene synonyms are not nececarillyunique. For instance
## $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"
## $MOG## $MOG$`4340`## [1] "MOG" "BTN6" "BTNL11" "MOGIG2" "NRCLP7"
