GeneList is a platform that makes it easy to navigate research resources. The GeneList R package lets you export a vector of gene Ids to gene-list.com using the function gene_list().

Using the R package devtools, run devtools::install_github('https://github.com/GeneList/GeneList', build_vignettes = TRUE)

Clone the repository, for example using git clone https://github.com/GeneList/GeneList.git.

Open R in the directory where you cloned the package and run install.packages("GeneList", repos = NULL, type "source")

library(GeneList)

# Input vector of gene Ids 
genes<-c("PIK3CA","KRAS","PTEN","BRAF")

# Export list of genes to gene-list.com 
gene_list(genes,genome="mouse",search_term="Cancer")

Identifiers can be gene symbols, Ensembl or UniProt accessions, Entrez ids, a GO term such as GO:0006281, or a chromosome range such as chr1:10000-5000000.

genome takes either the common name or the scientific name of any species below. Case and spacing are ignored, so "rat", "Rat", "Rattus norvegicus" and "rattus_norvegicus" are all the same genome. The default is human.

# The full table, with common names, scientific names and assemblies
gene_list_genomes()

# These are the same request
gene_list(c("Ccne1", "Trp53"), genome = "rat")
gene_list(c("Ccne1", "Trp53"), genome = "Rattus norvegicus")

# As are these
gene_list(c("AT1G01010", "AT1G01020"), genome = "thale cress")
gene_list(c("AT1G01010", "AT1G01020"), genome = "Arabidopsis thaliana")

An unrecognised genome raises an error listing the species available, rather than opening a page with no genes on it.

The site itself matches on one name per genome — a common name for some species and a scientific one for others — which is what gene_list_genomes()$genome holds. gene_list_genome() shows what a name resolves to:

gene_list_genome("Baker's yeast")
#> [1] "yeast"

gene_list_genome("Rat")
#> [1] "rattus_norvegicus"