Zero-shot prediction of drug responses using biologically informed neural networks trained on phosphoproteomic timeseries
Fig 4
Network analysis of non-canonical signaling.
A. Volcano plot of differentially expressed phosphosites between EGF-stimulation and SHP099 inhibition. Relevant phosphosites (FOXO3:S7, RASH:S35, MAPK14:T180, and PIK3CA:T508) are highlighted. B. Phosphorylation levels of FOXO3:S7 across two replicates. Full time series shown for EGF-stimulation; static data at 12 min for DMSO and SHP099 inhibition. Line indicates means; ribbon shows standard deviations; dashed line indicates DMSO-baseline; x shows the model prediction for the perturbed sample. C. Network visualization of the canonical RAS/MAPK pathway containing PTPN11 (SHP099 target), the PI3K/AKT pathway with FOXO3, and the potential crosstalk via p38 MAPK.