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 weekly since 8th of Match 2017

Available species are

  • Homo sapiens
  • Mus musculus
  • Rattus norvegicus
  • Danio rerio
  • Escherichia coli
  • Caenorhabditis elegans
  • Drosophila melanogaster
  • Rhesus macaque

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"       "AI837106"   "D6Ertd375e" "Eno-2"      "NSE"       
## 
## 
## $Mog
## $Mog$`17441`
## [1] "Mog"           "B230317G11Rik"
geneSynonym(c('Eno2','Mog'), tax = 10090)
## $Eno2
## $Eno2$`13807`
## [1] "Eno2"       "AI837106"   "D6Ertd375e" "Eno-2"      "NSE"       
## 
## 
## $Mog
## $Mog$`17441`
## [1] "Mog"           "B230317G11Rik"
mouseSyno(c('Eno2',17441))
## $Eno2
## $Eno2$`13807`
## [1] "Eno2"       "AI837106"   "D6Ertd375e" "Eno-2"      "NSE"       
## 
## 
## $`17441`
## $`17441`$`17441`
## [1] "Mog"           "B230317G11Rik"
humanSyno('MOG')
## $MOG
## $MOG$`4340`
## [1] "MOG"    "BTN6"   "BTNL11" "MOGIG2" "NRCLP7"