Synergy Maps: exploring compound combinations using network-based visualization

Table 3 Synergy metrics calculated for the NCATS malaria dataset

Synergy metric	Derivation
pGamma	Negative based-10 logarithm of Gamma, from Cokol et al. [25]
Median Excess	The median of the sum of the differences between the combination responses and the single agent responses
Num Excess	The number of combinations in a block that show a better combination responses than both the corresponding single agents
−ExcessHSA	Negative of ExcessHSA, from Lehár et al. [11]
−ExcessCRX	Negative of ExcessCRX, from Lehár et al. [11]
LS3 × 3	The minimum value of the sum of the deviations from the HSA model are evaluated on all 3 × 3 submatrices of the response matrix (excluding the single agent row and column)
pBeta	Negative based-10 logarithm of Beta, from Cokol et al. [25]

The synergy metrics for the dataset. These were calculated for a previous study, however a couple of alterations were required to get a consistent behaviour, specifically positive and negative values relating to synergy and antagonism respectively: pBeta and pGamma were derived from Beta and Gamma [25] by taking the negative based-10 logarithm. The original metrics specify synergy below 1, and antagonism above, so this transformation handily yields the desired mapping of antagonism to negative values. −ExcessHSA and −ExcessCRX are derived from ExcessHSA and ExcessCRX [11] by taking the negative in order to attribute positive values to synergistic interactions.

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