Fig. 5. Protein phosphorylation-kinase networks by SPHINKS reveal subtype-specific master kinases and signaling.

a, Heat map depicting the 70 highest significant outlier phosphorylated proteins in each functional GBM subtype (P < 0.005; BlackSheep). Unsupervised clustering and biological pathways significantly enriched are presented on the left (P < 0.01; Fisher’s exact test). The number (n) of GBM samples for each subtype is indicated. b, Global kinase–substrate phosphosite interactome inferred by SPHINKS. Nodes represent kinases and substrate phosphosites and lines their interactions. Kinase families and phosphorylated amino acid residues are indicated by different colors. Node size of the kinases is proportional to the number of interacting phosphosites. Yellow interactions indicate substrate phosphosites reported in the PhosphoSitePlus database; gray interactions are inferred new interactions. The number (n) of GBM samples is as in a. c, Circular plot depicting the most active kinases in each GBM subtype compared to all other subtypes (effect size > 0.3, P < 0.01; two-sided MWW test) with the outermost circle representing the color scale of kinase activity. The five predicted kinase-regulated phosphorylation sites with the highest SPHINKS score are indicated by black dots with SPHINKS score within the dashed line, > 0.95; SPHINKS score between dashed and continuous line, 0.95–0.90; and SPHINKS score inside the continuous line, < 0.90. The number (n) of GBM samples is as in a. d, Heat maps showing kinase activity (NES), MWW protein abundance score and MWW gene expression score of SPHINKS MKs specific for each CPTAC-GBM subtype (two-sided MWW test, n = 85 GBM samples). Heat maps depicting MWW gene expression score of the same kinases in single GBM cells (n = 17,367 single glioma cells) and PDOs (n = 79 PDOs) signify the cancer cell intrinsic expression of the top-scoring kinases identified by SPHINKS. Only values of logit(NES) > 0.58 are shown.