Fig. 6

Phosphoproteomic and proteomic analyses of TRAP-perturbed cells reveal regulation of cell adhesion and extracellular matrix organization network. GO Biological Process enrichment analysis of all the genes regulated upon TRAP perturbation (842 genes, Additional file 7: Table S2) compared to all the identified genes (9570 genes) (a). Enriched GO terms are displayed by significance of the enrichment (q-value, multiple testing corrected) and fold enrichment. Interaction network of proteins belonging to the GO terms “biological adhesion” and “extracellular matrix organization” and significantly regulated upon TRAP perturbation (b); interactions were retrieved from the STRING database. Squared shaped nodes represent proteins and round shaped nodes represent phosphorylation sites. Nodes fill color: log₂ transformed ratio (H/L) values for standard proteomics and phosphoproteomics analysis of TRAP3^high cells (Heavy SILAC labeled) compared to control cells (Light SILAC labeled) (replicate 1 and 2 average). Nodes border color: log₂ transformed ratio values for standard proteomics analysis of scrambled, TRAP sh2 and sh3 + 4 cells (average of sh2 and sh3 + 4 ratios relative to scrambled)