Repository containing the files and scripts required to reproduce the analysis presented in "Deciphering molecular mechanisms of synergistic growth reduction in kinase inhibitor combinations" preprint.
In all scripts, the following abbreviations have been used for the drugs:
PD - MEK inhibitor
PI - PI3K inhibitor
5Z - TAK1 inhibitor
PIPD - PI3K/MEK combination
PI5Z - PI3K/TAK combination
The following scripts have been used to prepare the manuscript figures:
Phosphoproteomics/scr/PCAS.R - Figure 2B
Phosphoproteomics/scr/logFC_corr.R - Supplementary Figures
Transcriptomis/scr/PCAs.R - Figure 5A
Transcriptomis/scr/tr_logFC_corr_septp.R - Figure 5A
Transcriptomis/scr/tr_TF_activities_all_ulm.R - Figure 5B, 5C, Supplementary Figures
Transcriptomis/scr/tr_visualize_synergy_DEGs.R - Figure 5D
Transcriptomis/scr/tr_viz_metabolic_pathway.R - Figure 6, Supplementary Figures
NB! All data and scripts will be uploaded to Zenodo upon publication