Supplementary Figure 9: Kinase network topologies and kinase activities associated to kinase protein expression and phosphorylation. | Nature Biotechnology

Supplementary Figure 9: Kinase network topologies and kinase activities associated to kinase protein expression and phosphorylation.

From: Reconstructing kinase network topologies from phosphoproteomics data reveals cancer-associated rewiring

Supplementary Figure 9

(a) Kinase protein expression, phosphorylation extent (calculated as the sum of intensities of peptides or phosphopeptides, respectively, derived from a given kinase) or their ratio was correlated to the enrichment of edges defined by the same kinase (top graphs) or to the predicted kinase activity (bottom graphs). Numbers refer to positively correlated edges (Spearman r > 0, bottom row) or those with Spearman r >0.28 (p<0.01, top row). Network edge enrichment as well as protein and phosphoprotein expression were calculated for 30 primary AML cases and for 83 primary breast cancer samples from a meta-analysis of their proteomes and phosphoproteomes from Casado et al. (Leukemia 32, 1818-1822, 2018) and Mertins et al. (Nature 534, 55-62, 2016). Violin plots show the kernel density of the data, in which probability is related to the width of the plot. Boxplots within violin plots (top graphs) show the median, interquartile ranges, and max-min ranges. Statistical significance of differences between the spearman rank values for each analysis was calculated using a two-sided Kruskal-Wallis test. (b) Association between number of kinase downstream targets (PDTs) and the correlation of kinase activity with phosphokinase expression. (c) Relationship between number of phosphorylation sites detected in kinase with the association between kinase activity and phosphokinase expression. (d) Relationship between number of phosphorylation sites detected in kinase with the association between kinase activity and the expression of unmodified kinase. P-values were calculated using Pearson (n=69 ovarian samples).

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