Additional file 3 of A network-based drug prioritization and combination analysis for the MEK5/ERK5 pathway in breast cancer

Additional file 3: Supplementary Table 1. List of genes associated with the MEK5/ERK5 signalling pathway and enriched in human breast tissue. These genes were obtained after merging evidence from the DisGeNet and the Human Proteome Atlas databases. Supplementary Table 2. Topology analysis of plant polyphenols target MEK5/ERK5 pathway networks. Disease association information was extracted from the DisGeNet database with only genes curated in breast cancer selected. Nodes with low betweenness centrality scores (betweenness = 0) were removed. Supplementary Table 3. Pathway enrichment analysis results based on KEGG, GO, and DisGeNet showing the enriched terms in the nodes of subnetworks of each plant polyphenol. Supplementary Table 4. Results of drug-target subnetwork topological analysis showing the number of proteins (nodes) and their interactions (edges) at different doses. Supplementary Table 5. List of enriched pathways in the set of common genes between plant polyphenol and breast cancer target subnetworks. Supplementary Table 6. Differences between the network topology and overall average network topology for each plant polyphenol target network. Supplementary Table 7. List of drugs prioritized as combination candidates with target network synergistic effects. Different dosages of each drug were used in the simulation and for each dose the first 10 best scored drugs are provided. The network scores as well as the number of genes in common between drug-deregulated genes and the background network are shown. Supplementary Table 8. List of drugs prioritized as combination candidates with target network enhancer effects. Different dosages of each drug were used in the simulation and for each dose, the first 10 best scored drugs are provided. The network scores as well as the number of genes in common between drug-deregulated genes and the background network are shown.