Phosphorylation of protein complexes
Annotations for protein complexes were obtained from CORUM v3.0 database (Giurgiu et al., 2019). Overall significance of changes of phosphosites of a protein complex was inferred from the log2 fold change of individual phosphosites of protein members of the complex using the same Z-test based approach described for estimation of kinase activities. Among the 3512 complexes, 1070 complexes with phosphorylation changes obtained from 4 or more phosphosites were considered. Of these, 67 complexes had significant phosphorylation change (-log10(p value) from Z-test > 2.5) in at least one time point. In order to select non-redundant complexes, we first constructed a complex term tree based on distances (1-Jaccard Similarity Coefficients of shared genes) between the significant complexes. The term tree was cut at a specific level (h = 0.99) to identify clusters of non-redundant complexes. The largest complex was selected from each cluster.