Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In
Question: Genes by Protein Domain
2
gravatar for H.Hasani
4.8 years ago by
H.Hasani • 980
Freiburg, Germany
H.Hasani • 980 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 COMMENT • link •
modified 4.8 years ago by Matt Miossec • 350 • written 4.8 years ago by H.Hasani • 980
3
gravatar for Matt Miossec
4.8 years ago by
Matt Miossec • 350
UK/Oxford/Wellcome Centre for human genetics
Matt Miossec • 350 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 COMMENT • link modified 4.8 years ago • written 4.8 years ago by Matt Miossec • 350
2

Thanks! Exactly what I was looking for.

ADD REPLY • link written 4.8 years ago by H.Hasani • 980

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 REPLY • link written 4.8 years ago by GenoMax ♦ 96k

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 REPLY • link written 4.8 years ago by H.Hasani • 980
2
gravatar for GenoMax
4.8 years ago by
GenoMax ♦ 96k
United States
GenoMax ♦ 96k wrote:

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

WD40 Example: https://www.ebi.ac.uk/interpro/entry/IPR001680/proteins-matched
ADD COMMENT • link written 4.8 years ago by GenoMax ♦ 96k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1142 users visited in the last hour
_