Fig. 4.

Enriched protein groups within co-modified targets upon proteasome inhibition. A, Volcano plot showing a group of known STUbL targets in red identified among the significantly co-modified proteins upon MG132 treatment, which are highlighted in blue. B, Gene ontology analysis revealed significant enrichment for various biological processes among the identified co-modified targets upon MG132 treatment. For a selection of these processes the FDR value of their enrichment is shown as a -Log10(FDR). C, like B, but showing the enrichment factor for each of the selected biological processes. D, Co-modified proteins annotated among the biological process of transcription were identified and their interactions based on the STRING database as shown. Larger circle size corresponds to a lower q value and darker color indicates a higher difference. E, like D, but showing co-modified proteins annotated to the biological process of DNA repair. F, Co-modified proteins annotated to the biological process of the cell cycle, including targets involved in the more specific process of mitotic cell cycle (orange outline). Larger shape size corresponds to a lower q value and darker color indicates a higher difference.