Supplementary Figure 5: Validation of groups of phosphorylation sites as markers of kinase network edges. | Nature Biotechnology

Supplementary Figure 5: Validation of groups of phosphorylation sites as markers of kinase network edges.

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

Supplementary Figure 5

(a) Motif enrichment analysis in phosphorylation site groups that define the named network edges. Z-scores values are shown in y-axes and x-axes show the number of phosphopeptides with the labeled motif. For clarity not all data-points are labeled. Enrichment was calculated as in Supplementary Fig. 3. (b) Enrichment of kinase network axes as a function of treatments with EFG or IGF-I for the indicated times. (c) Enrichment of phosphopeptides in the named edges in predicted kinase-substrate (Netphorest) groups. Enrichment was calculated as in Supplementary Fig. 3. (d) Enrichment of edges in P31/Fuj as a function of treatments with the named kinase inhibitors; z-scores were calculated using the PAGE method as in (BMC Bioinformatics 6, 144, 2005) and (PNAS 112, 7719-7724, 2015) and p-values using a two-sided Kolmogorov-Smirnov test as in (PNAS 102, 15545-15550, 2005). FDR was calculated by adjusting p-values for multiple testing using the Benjamini-Hochberg method (n = 2 independent experiments performed in technical replicate).

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