Table 2.

Results of TRANSACT compared to four competing approaches—ElasticNet, DL, ComBat ± DL, and PRECISE—for six drugs on HMF

GDSC		HMF				p-val [effect size] on HMF
Drug	Samples	Drug	Samples			Elastic Net	DL	DL + ComBat	PRECISE	TRANSACT
			PR	SD	PD
Afatinib	800	Trastuzumab	25			0.18	0.069	0.13	0.021	0.032
			9	11	3	[0.70]	[0.81]	[0.74]	[0.93]	[0.89]
Irinotecan	796	Irinotecan	67			0.060	0.060	0.082	0.10	0.020
			5	34	25	[0.73]	[0.75]	[0.71]	[0.69]	[0.80]
Cisplatin	764	Carboplatin	64			0.23	0.051	0.054	0.59	0.0045
			22	27	12	[0.58]	[0.68]	[0.67]	[0.67]	[0.78]
5-Fluorouracil	801	5-Fluorouracil	61			0.065	0.14	0.14	0.21	0.24
			10	33	18	[0.68]	[0.63]	[0.63]	[0.59]	[0.58]
Paclitaxel	753	Paclitaxel	45			0.56	0.30	0.34	0.39	0.061
			14	19	9	[0.48]	[0.43]	[0.43]	[0.53]	[0.70]
Gemcitabine	752	Gemcitabine	50			0.039	0.019	0.039	0.0089	0.0042
			22	17	9	[0.71]	[0.74]	[0.71]	[0.78]	[0.81]

For each drug, we train five predictors and compare in each scenario the predicted AUC to the known clinical response using one-sided Mann–Whitney U test between PR and PD (Methods). For each predictor, we report the P value and the effect size (area under the ROC, effect size associated with the Mann–Whitney U test) in brackets. Italic cells correspond to significant associations (P < 0.05). Bold cells correspond to significant associations with the largest effect size across the five methods.