Phosphorylation value at protein level

Question

[guiu]

Hello everyone,

I would like to map phosphoproteomics data on a signaling network where each node is a protein, and use the phosphorylation as a proxy for protein "activation".

The phosphorylation occurs at phosphosite level, where one protein can have multiple sites, and each phosphorylation can have a different biological role. So I see why differential phosphorylation analysis is done for each phosphosite separately, and only the biological interpretation of the results (e.g. GO enrichment) is done using the proteins to which the phosphosites map. Nevertheless, I am doubting if having a protein-level value would be biologically non-sense.

So my question is: Does it make any sense to try and summarize at gene level the phosphorylation values? Is there any accepted approach to do this?

[natasha.sernova]

See these papers:

Mapping and analysis of phosphorylation sites: a quick guide for cell biologists

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3583658/

But mapping here has a little bit different meaning...

I found several articles, where people talk about phosphorylation level for proteins:

Here - diabetic patients

https://www.ncbi.nlm.nih.gov/pubmed/23026841

Significant correlation between the acceleration of platelet aggregation

and phosphorylation of HSP27 at Ser-78 in diabetic patients.

The authors of the following paper try to predict phosphorylation level from gene expression:

https://academic.oup.com/bioinformatics/article/31/4/462/209066/Predicting-protein-phosphorylation-from-gene

Predicting protein phosphorylation from gene expression: top methods from the IMPROVER Species Translation

Challenge

Here p53 phosphorylation is considered:

http://sra.dbcls.jp/search/view/SRP002486

Role of p53 serine 46 in p53 target gene regulation. And see links at the bottom of the page.

But I have seen something about network and phosphorylation only in the article below:

http://sci-hub.cc/10.1126/scisignal.2002093#

Sequence, Structure, and Network Evolution of Protein Phosphorylation

[guiu]

Hi Natasha, thanks, I will look carefully into the IMPROVER challenge. The other links confirm what I was saying: the analysis these days is done at the phosphosite level.