Question: lift over gene ids rat to human
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gravatar for sim.j.baum
2 days ago by
sim.j.baum50
sim.j.baum50 wrote:

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

rna-seq biomart R • 44 views
ADD COMMENTlink modified 2 days ago • written 2 days ago by sim.j.baum50
0
gravatar for sim.j.baum
2 days ago by
sim.j.baum50
sim.j.baum50 wrote:

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

ADD COMMENTlink written 2 days ago by sim.j.baum50
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