Fig. 3: Identification of co-expression cluster regulators and antagonizing chemical compounds.

a Network diagram showing the minimal set of edges that connect all co-expression modules and cell lines and that were identified using a minimal spanning tree analysis performed on the binary adjacency matrix representing the full set of interactions between all modules and all cell lines. Co-expression modules and cell lines are indicated respectively as diamonds labeled by module number (i.e., M1 to M22) and circles labeled by cell line name. The edges connecting all cell lines through a minimal set of co-expression modules are indicated in red. b Results identifying upstream regulators (Y-axis) for each of the five co-expression modules that connect all IBC cell lines (X-axis) are shown in heatmap format. At the intersection between rows and columns, cells are color-coded as shown in the legend only when the difference between the co-expression module specific connectivity Scores (CSs) for overexpression and knockdown of the respective genes exceeds 150 (i.e., at least 75 upon overexpression and at most -75 upon knockdown). c Results identifying target/drug combinations (Y-axis) for each of the five co-expression modules that connect all IBC cell lines (X-axis) are shown in heatmap format. At the intersection between rows and columns, cells are color-coded as shown in the legend only when the difference between the co-expression module specific CSs for overexpression of the drug target and drug treatment exceeds 150 (i.e., at least 75 upon overexpression of the target and at most −75 upon treatment).