Fig. 1

(A) Example BPM graph motif in the original Kelley and Ideker (unweighted) setting. Here nodes a-e form compensatory pathway 1 and f-h compensatory pathway 2; completing either pathway 1 or 2 is necessary for the cell to be viable. Solid lines are physical interaction edges, and dashed lines are synthetic lethality edges. Note that pathway 1 also has internal redundancy (only one of paralogs b and c is necessary to complete pathway 1) so that interactions between b or c and the nodes of pathway 2 is not lethal. We have colored the true synthetic lethality relation from g to e red to represent that perhaps this pair wasn’t tested and so that edge is missing from our data. (B) In the weighted setting, we consider genetic interaction edges only. Edges have both positive (purple) and negative (black) genetic interaction weights, with strength of line indicating relative magnitude of the edge weight. Within each pathway we have a near clique of low-weight positive interaction edges. The red edge indicates that the edge from e to c is erroneously reported as missing because it was not tested or below the noise threshold. In this setting, the pattern of negative interaction edges shows deleting a, d, or e together with a pathway 2 gene gives a synthetic growth defect (negative weight of smaller magnitude than the lethality edges in A), but deleting b or c and a pathway 2 gene gives growth similar to wildtype.