Fig. 2

Flowchart of the three scoring methods. We devised three scores to rank the drug combinations in terms of synergy according to the gene expression profiles obtained from individual treatments. Two of the scores (co-gene and co-GS) were computed by the degree of overlap in disturbed genes or enriched gene sets between two drugs. Here activities and significance of changes in gene sets were modeled by a gene set enrichment analysis. For the co-gene/GS score of a drug pair, we computed an average percentage of overlapped genes across all commonly enriched gene sets. Drug pairs were ranked based on each of the prediction scores