Using Phosphorylation Data To Validate Gene Regulatory Interactions

Question

[pegahtv]

I have already made a gene regulatory network for several species, by textmining, and I want to use phosphrylation data to validate these networks.

1) Does it make sense and is it possible?

2) I downloaded some datasets from http://www.peptideatlas.org/speclib/index.php#ISB but I have no idea how to use them. Could someone help me about it?

Thanks for your help.

Answer 1

[Alex Paciorkowski]

Just a couple of comments:

1) Phosphorylation events are not the only ways gene regulatory networks may function, so if you only plan on looking at that -- depending on your network -- you may miss other significant interactions. For example, if transcription factors are involved if you are not measuring downstream gene expression in some way validation of your network will be incomplete.

2) What datasets did you download from the peptideatlas, and to what purpose? It is hard to give pointers about how to use them, when it's not clear what types of files they are, and what your proposed workflow is. Some more details might help.