Fig. 2: Activity landscapes of pathways and kinases functionalize proteins/p-sites.
From: Proteome activity landscapes of tumor cell lines determine drug responses
a Activity landscape of cellular pathways for the CRC65 panel (n = 64 cell lines) and b of kinases for the NCI60 panel (n = 60 cell lines; Supplementary Methods). Relative activity ranges from 0 to 1 representing minimal and maximal relative activity, respectively. Areas of high activity are labelled. c, d Waterfall plots visualizing the relative activity of kinases in c K562 cells and d SR cells. The kinases with the highest relative activity are highlighted. The color of the data points corresponds to the color scale of panel b. Relative activity ranges from 0 to 1 representing minimal and maximal relative activity, respectively. e Hive plot showing significant associations between groups of functionally related proteins/p-sites, cell lines with the same MSI status and groups of abundance-related proteins/p-sites (highly correlated proteins and p-sites) identified by weighted gene correlation network analysis in the CRC65 dataset (Supplementary Methods). Colored edges (blue = MSI+, red = MSI−) represent significant associations between corresponding nodes on all three axes. f Volcano plot visualizing single proteins/p-sites from colored groups of abundance-related proteins/p-sites in c, which show significantly higher abundance in MSI+ (n = 17; blue) or MSI− (n = 47; red) cells (Benjamini–Hochberg corrected P < 0.05, moderated t-test). Proteins/p-sites in the top right corner are highly abundant in MSI− cell lines and their functional annotations are shown in the magnification (right panel). The light red color in the right panel (In databases+) indicates proteins/p-sites, which are part of the functional annotations enriched in the corresponding group of abundance-related proteins/p-sites from C (e.g., MSH2), while the solid red color (In databases−) highlights proteins/p-sites for which we suggest new functional annotations using guilt-by-association (e.g., ASXL2_pS1319). Shaded areas highlight proteins/p-sites with common functions (blue text). Source data are provided as a Source Data file.
