Are there tools for Pathway/Functional Enrichment with Respect to Differential Phosphorylation

Question

[pld]

I have some differential phosphorylation data that I would like to do functional, pathway or similar types of enrichment. However, it seems most such tools focus specifically on gene expression or protein expression. I can measure fold changes in protein expression, but I would really like to include phosphorylation information.

Does anyone have any suggestions?

Answer 1

[Devon Ryan]

Many of the pathway/functional enrichment packages would work fine with differential phosphorylation data, since they often just need lists of significant and non-significant changes (often they just end up doing a hypergeometric test). One example online tool would be David.

[pld]

The problem with just dumping this into gene expression tools is that there is noting capturing changes in non-phosphoylated protein levels versus phosphorylated protein levels across conditions.

Eg:

NFkB:       PHOS       NO-PHOS

INF          a            b

UINF        c            d

That is, there is a difference between changes in protein expression and changes in phosphorylated protein levels. I realize that there isn't anything that can handle the combinatorial aspects of phosphorylation but I was hoping to capture at least some of the pathway state. Protein expression generates the nodes in a pathway, but phosphorylation applies control over the edges in those pathways.