Genes by Protein Domain

Question

[H.Hasani]

Hello biostars,

I'm wondering if there is a way to find all genes sharing the same protein domain, e.g. the WD repeat domain containing occurs in many genes: BUB3, CDC20, DDB2, etc.

Is there a way I can retrieve the full list of genes having domain XX in common?

Thank you in advance!

Answer 1

[Matthieu Miossec]

Any time you want to produce a list of some description, try using BioMart first:http://www.ensembl.org/biomart/

Once you've selected which gene dataset you want to look at (e.g. Homo Sapiens (GRCh38.p5) from Ensembl Genes 84), you can go to Filters > PROTEIN DOMAINS AND FAMILIES > Limit to genes with these family or domain IDs and type in your domain.

You'll find BioMart comes in handy for a large number of tasks.

[H.Hasani]

Thanks! Exactly what I was looking for.

[GenoMax]

A Minor point but significant based on the original question.
Doing it this way does not select all proteins, irrespective of what genome they are from.

[H.Hasani]

Thanks! I'm not really interested in the protein, instead in the genes having the same protein domain of my choice. Thanks to you both.

Answer 2

[GenoMax]

From InterPro: https://www.ebi.ac.uk/interpro

WD40 Example: https://www.ebi.ac.uk/interpro/entry/IPR001680/proteins-matched