Supplementary Figure 4: Kinase signaling analysis using PDTs and previous databases of kinase-phosphosite relationships. | Nature Biotechnology

Supplementary Figure 4: Kinase signaling analysis using PDTs and previous databases of kinase-phosphosite relationships.

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

Supplementary Figure 4

(a) Number of downstream targets of kinases poorly annotated in previous databases of K-P relationships. (b) Number of K-P relationships and number of kinases present in different databases of K-P relationships. (c) Experimental design of phosphoproteomic experiment of P31/Fuj cells treated with the named kinase inhibitors, and summary of results. P-values were calculated using two-sided paired t-test of log transformed data and FDR was calculated by adjusting p-values for multiple testing using the Benjamini-Hochberg method. These statistics were applied to the mean phosphoproteomics data of two independent experiments performed in technical replicate. (d) Results of changes in kinase activities as a function of treatment with the named kinase inhibitors (as determined by KSEA) when using different databases of K-P relationships as input of the KSEA algorithm. 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.

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