How to extract gene families for a given set of genes

Question

[noorpratap.singh]

I have different set of genes for mouse. For each set I want to characterize the number of gene families each set belongs. I thought extracting the family label might be trivial from Ensembl using R Package biomaRt. But I no longer see family as an attribute available in the ListAttributes. It does seem that one could extract families from the earlier versions of biomaRt. I was wondering if someone was familiar that why biomaRt does not provide this functionality any longer. Also, what could be other possible avenues to extract gene families?

Answer 1

[Ben_Ensembl]

Hi noorpratap,

The gene and protein families have been retired since Ensembl 102: https://www.ensembl.info/2020/11/24/gene-and-protein-families-retiring/

However, you can still access this data through the BioMart web and Ensembl REST API archives: [1] https://aug2020.archive.ensembl.org/index.html [2] https://aug2020.rest.ensembl.org/documentation/info/family_member_id

[noorpratap.singh]

Hi Ben,

Thanks for the message, I will try to follow these resources.