How to extract gene families for a given set of genes
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6 days ago

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?

gene mus musculus. family biomart ensembl • 219 views
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3 days ago
Ben_Ensembl ★ 2.0k

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

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Hi Ben,

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

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