Question: Gene Names Of All Proteins Having A Tyrosine Residue
0
gravatar for Stephen
7.1 years ago by
Stephen2.7k
Charlottesville Virginia
Stephen2.7k wrote:

Simple question - I want the names of all the genes that have a tyrosine residue in their respective amino acid sequence.

Bonus points - limit that to only genes having a tyrosine that is able to be phosphorylated by a tyrosine kinase (I understand these recognize some kind of motif, not just any old tyrosine).

Background: I'm trying to do a GO-style hypergeometric overrepresentation analysis of significantly differentially expressed proteins that are pulled down with an anti-phosphotyrosine antibody. An appropriate background set would not be every gene in the genome - only those containing a phosphorylatable tyrosine.

proteomics • 1.5k views
ADD COMMENTlink modified 7.1 years ago by Chris Evelo10.0k • written 7.1 years ago by Stephen2.7k
1

http://gps.biocuckoo.org/links.php has a lot of resources. Not sure how out of date they are though.

ADD REPLYlink written 7.1 years ago by Damian Kao15k
0
gravatar for Chris Evelo
7.1 years ago by
Chris Evelo10.0k
Maastricht, The Netherlands
Chris Evelo10.0k wrote:

Well the first part should indeed be easy. Just get all protein sequences for your species of interest (from UniProt, or whatever you are happy to use ) and scan these for "Y". You could even use grep for that.

(Ohh, and don't forget to get the ID's and the names as well).

ADD COMMENTlink modified 7.1 years ago • written 7.1 years ago by Chris Evelo10.0k

General idea is good but 'T' is threonine, 'Y' is tyrosine

ADD REPLYlink written 7.1 years ago by Cliff Beall450

Thanks Cliff, edited, must have been my jetlag.

ADD REPLYlink written 7.1 years ago by Chris Evelo10.0k
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