Gene Names Of All Proteins Having A Tyrosine Residue

Question

[Stephen]

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.

[Damian Kao]

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 Not sure how out of date they are though.

Answer 1

[Chris Evelo]

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).

[Cliff Beall]

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

[Chris Evelo]

Thanks Cliff, edited, must have been my jetlag.