Question: Genes by Protein Domain
2
gravatar for H.Hasani
4.8 years ago by
H.Hasani980
Freiburg, Germany
H.Hasani980 wrote:

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!

protein gene • 988 views
ADD COMMENTlink modified 4.8 years ago by Matt Miossec350 • written 4.8 years ago by H.Hasani980
3
gravatar for Matt Miossec
4.8 years ago by
Matt Miossec350
UK/Oxford/Wellcome Centre for human genetics
Matt Miossec350 wrote:

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.

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by Matt Miossec350
2

Thanks! Exactly what I was looking for.

ADD REPLYlink written 4.8 years ago by H.Hasani980

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.

ADD REPLYlink written 4.8 years ago by GenoMax96k

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.

ADD REPLYlink written 4.8 years ago by H.Hasani980
2
gravatar for GenoMax
4.8 years ago by
GenoMax96k
United States
GenoMax96k wrote:

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

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

ADD COMMENTlink written 4.8 years ago by GenoMax96k
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