BiomaRt Many to Many Relationship filtering

Question

[iislam]

Hi all! I am hoping to get a file containing 1:1:1:1:1:1 orthologs across human, mouse, chicken, rat, rabbit, possum, and macaque. I used these BiomaRt options

But I have a problem.

In the CSV list that BiomaRt gave me, I have these annoying many-to-many relationships. I want each gene to only occur once throughout the species columns. Some genes however, are highly repeated. I used python to filter this list and got that only 1781 out of 1901282 lines are unique. Can someone try to give me advice on how to get orthologs across these species in a way where these annoying many-to-many relationships do not occur? I don't believe that there are 1781 genes that are orthologous to each other in these 7 species. plz help, what do I do? I am a lowly grad student with a phenomenal task. Pls help #wannacry

[GenoMax]

Have you looked at NCBI's homologene database? You can get more or less one to one orthologs from many species. Here is an example of GAPDH gene.

Answer 1

[Ben_Ensembl]

Hi iislam,

This is possible with BioMart, although it will take a few steps. You will need to get the 1:1 orthologues between human and every other species separately, then join all files and select the lines that have every species.

In each BioMart query, you will need to add the Filter: Multi species comparisons -> Homologue filters -> Orthologous Mouse Genes -> Only

Then add the 'Mouse homology type' attribute.

You can then filter your results to only contain 1:1 ortholgues.

You can then perform this query for each species against human, then join all files and select the lines that have every species.

Best wishes

Ben Ensembl Helpdesk