Gene symbol of chinese hamster

Question

[rykerklie7]

I am trying to convert gene symbol of chinese hamster to rat and tried this:

hamster = useMart("ensembl", dataset = "cgcrigri_gene_ensembl")
rat = useMart("ensembl", dataset = "rnorvegicus_gene_ensembl")

hamster_genesymbol = annot_chinese_hamster$external_gene_name # gene list to lift over

genesV2_hamstertorat = getLDS(attributes = c("CHO_symbol"), 
             filters = "CHO_symbol", 
             values = hamster_genesymbol , 
             mart = hamster, 
             attributesL = c("rgd_symbol"), 
             martL = rat, 
             uniqueRows=T)

However, just like "hgnc" symbol is for humans, "mgi" is for mouse, "rgd" for rat am unable to find the abbreviation for cgcrigri. I tried list attributes and notice "cho" and tried that but does not work. Any suggestions?

Answer 1

[Jean-Karim Heriche]

I would do it like this:

hamster <- useMart("ensembl", dataset = "cgcrigri_gene_ensembl")
hamster_genesymbols <- c("Stap1", "Tmprss11a", "Ythdc1")
getBM(attributes = c('rnorvegicus_homolog_associated_gene_name'), filter = 'external_gene_name', mart = hamster, values = hamster_genesymbols)