Looking for phosphoproteomics data for kinase inhibited states

Question

[richard.carr.3rd]

I am looking for a database or a way that I could look at broad changes in protein phosphorylation by phosphoproteomics at many targets in a kinase inhibited or a kinase knockdown state. For example, all the proteins that show reduced phosphorylation when Akt (or any given kinase) is inhibited or knocked-down or out.

Any help would be very much appreciated.

Thanks!

Answer 1

[Pedrobeltrao]

There is no such database for human. Phosphogrid (phosphogrid.org) contains conditional phosphoproteomics data for yeast but even in that case you don't get the actual quantitative scores so there is no easy way to get these types of data right now except to compile them from articles. Pedro Cutillas has published several studies doing exactly what you want. The two recent papers you might want to have a look are these two:

1. Large-scale models of signal propagation in human cells derived from discovery phosphoproteomic data
2. Empirical inference of circuitry and plasticity in a kinase signaling network

There are other studies with fewer inhibitors.We have compiled several of them and we are now trying to publish meta analysis of these types of data. We will make all of the data available under the same protein ID system when that first manuscript gets closer to publication.

Answer 2

[Ibrahim Tanyalcin]

Dear Richard,

Try looking into Cytoscape (free) or Ingenuity Pathway (IPA-not free) software. I know that these two are used in pathway analysis. There is also STRING-DB, that can also be useful in your case.

I hope this helps,

Regards

Answer 3

[5utr]

PhosphositePlus has a downloadable table of Kinase-Substrate in different mammalian organisms: http://www.phosphosite.org/staticDownloads.do