Hello BC community,
I am trying to convert a list of human genes to mouse homologs using R. Biomart finds homologs of some genes but not others. I can't seem to figure out the reason for this behavior. An example code is below.
human = useMart("ensembl", dataset = "hsapiens_gene_ensembl") mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl") getLDS(attributes = c("external_gene_name"), filters = "external_gene_name", values = c("TP53", "MIR155HG", "STAT1", "PDCD1"), mart = human, attributesL = c("external_gene_name"), martL = mouse) # Gene.name Gene.name.1 #1 TP53 Trp53 #2 PDCD1 Pdcd1 #3 STAT1 Stat1
I tried the query using other arguments such as
hgnc_symbol and the results were the same. I know that MIR155HG should be conserved between human and mouse. This is confirmed by Mir155hg Ensembl page. I have several other genes like this that don't get mapped to the mouse genome for some reason.
What am I missing here?