Sheep-Human ortholog mapping with BioMart and Orthogene/Gprofiler

Question

[Michael]

Hi all,

I am having difficulty mapping gene Ensembl IDs from the Ovis Aries Texel breed genome (Oar_v3.1) to human orthologs. I have tried multiple approaches, using both BioMart and the Orthogene/gprofiler packages. Below is my approach using BioMart (thanks Kevin Blighe ) , which yielded the following:

sheep_ensembl <- useMart('ensembl', dataset = 'oaries_gene_ensembl')
human_ensembl <- useMart('ensembl', dataset = 'hsapiens_gene_ensembl')
annot_table <- getLDS(
  mart = sheep_ensembl,
  attributes = c('ensembl_gene_id','external_gene_name'),
  martL = human_ensembl,
  attributesL = c('ensembl_gene_id','external_gene_name','gene_biotype'))

Error in getLDS(mart = sheep_ensembl, attributes = c("ensembl_gene_id",  : 
  Query ERROR: caught BioMart::Exception::Query: returning undef ... missing attributes for your exportable?

Using Orthogene with gprofiler method, I get a dataframe with all N/A for ortholog genes. I have tested with genes from the Ovis Rambulliet species and am able to get mappings. Does ortholog mapping for Oar_v3.1 just not exist?

Thanks!

[Shuang He]

It seems that the homologs page does not exist.

grep('homologs',listAttributes(sheep_ensembl)) integer(0)