Fig. 5: Analysis of label-free quantification data and kinase activity profiling. | Nature Communications

Fig. 5: Analysis of label-free quantification data and kinase activity profiling.

From: Spike-in enhanced phosphoproteomics uncovers synergistic signaling responses to MEK inhibition in colon cancer cells

Fig. 5

A Kinase signature enrichment analysis of synergistic profile clusters from hierarchical clustered label-free data. Z-scored intensity profiles of treatment conditions within clusters. Data represented as mean ± standard deviation. Kinase signatures selected from PhosphoSitePlus and iKiP-DB. Size and color of points indicate number of precursors and significance (Fishers’ exact test), respectively. Biological replicates as indicated in Fig. 4. B Selected results from PTM-SEA using PhosphoSitePlus (PSP) and iKiP-DB kinase signatures, denoted by (P) and (i), respectively. PTM-SEA input consists of fold change signed p-values from limma moderated t-test (two-sided), filtered for phosphopeptides with moderated F-test (two-sided) p-value < 0.1, indicating significant regulation in at least one test. ES = enrichment score as calculated by PTM-SEA. Significance is denoted by asterisks, with * p < 0.1, ** p < 0.05, *** p < 0.01. C Kinase Library S/T (Serine/Threonine) Kinase Motif Enrichment Analysis. To derive ‘foreground’ phosphosites, moderated t-test results were filtered for a fold change (FC) > 0.1 and a p-value < 0.05. The output is the enrichment value (EV). Results for interaction test are depicted. Source data are provided as a Source Data file.

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