lift over gene ids rat to human

Question

[sim.j.baum]

Hi,
I am seeking to lift over gene IDs from rat to human, this is what I got:

library("biomaRt") 

human = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
rat = useMart("ensembl", dataset = "rnorvegicus_gene_ensembl")

x = c("Tll1", "Tlx3") # gene list to lift over

genesV2 = getLDS(attributes = c("mgi_symbol"), 
                 filters = "mgi_symbol", 
                 values = x , 
                 mart = rat, 
                 attributesL = c("hgnc_symbol"), 
                 martL = human, 
                 uniqueRows=T)


genesV2

I found several entries for the lift over between mouse and human, but not rat and human. Hope that for people working good time with biomaRt, this could be easy to solve. I will keep on searching in the mean time.

thank you & best wishes

Answer 1

[Mike Smith]

Cool that you got another solution. The issue in your original biomaRt approach is that the MGI Symbol is specifically for the mouse genome, in the same way that HGNC Symbol relates to the human genome. For rat you need to use the RGD Symbol. Otherwise, your code looks great e.g.

library("biomaRt") 

human = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
rat = useMart("ensembl", dataset = "rnorvegicus_gene_ensembl")

x = c("Tll1", "Tlx3") # gene list to lift over

genesV2 = getLDS(attributes = c("rgd_symbol"), 
                 filters = "rgd_symbol", 
                 values = x , 
                 mart = rat, 
                 attributesL = c("hgnc_symbol"), 
                 martL = human, 
                 uniqueRows=T)

genesV2
#>   RGD.symbol HGNC.symbol
#> 1       Tll1        TLL1
#> 2       Tlx3        TLX3

Answer 2

[sim.j.baum]

I took another route:

library(msigdbr)

m_df = msigdbr(species = "Rattus norvegicus")

m_df_sub = m_df[,c(5,8)] # select only the gene ids necessary
m_df_sub_dis = distinct(m_df_sub) # remove non unqique rows

df = merge(x = df, y = m_df_sub_dis, 'gene_symbol', all.x = TRUE)

At the end this gave me the human gene symbols for the respective rat gene symbols