Table 1.

Results of TRANSACT compared to four competing approaches—ElasticNet, DL, ComBat ± DL, and PRECISE—for 17 drugs on TCGA

GDSC		TCGA			p-val [effect size] on TCGA
Drug	Samples	Drug	Samples		Elastic Net	DL	DL + ComBat	PRECISE	TRANSACT
			Resp.	NR.
Afatinib	800	Trastuzumab	16		0.089	0.034	0.034	0.026	0.016
			14	2	[0.82]	[0.93]	[0.93]	[0.96]	[1.00]
Bleomycin	856	Bleomycin	53		0.15	0.17	0.47	0.11	0.091
			47	6	[0.63]	[0.62]	[0.51]	[0.66]	[0.67]
Cetuximab	868	Cetuximab	19		0.12	0.52	0.45	0.45	0.077
			9	10	[0.67]	[0.50]	[0.52]	[0.52]	[0.70]
Cisplatin	764	Cisplatin	308		1.1E-6	2.0E-4	1.1E-2	2.2E-5	3.9E-7
			242	66	[0.69]	[0.64]	[0.59]	[0.66]	[0.70]
Cisplatin	764	Carboplatin	166		0.042	0.15	0.69	0.024	0.0035
			111	55	[0.58]	[0.55]	[0.48]	[0.59]	[0.63]
Cyclophosphamide	747	Cyclophosphamide	102		0.57	0.62	0.85	0.11	0.64
			96	6	[0.48]	[0.46]	[0.38]	[0.65]	[0.46]
Docetaxel	665	Docetaxel	102		0.62	0.30	0.73	0.78	0.11
			67	35	[0.48]	[0.53]	[0.46]	[0.46]	[0.58]
Doxorubicin	871	Doxorubicin	101		0.81	0.0048	0.52	0.99	0.054
			68	33	[0.45]	[0.66]	[0.50]	[0.32]	[0.60]
Etoposide	880	Etoposide	84		0.21	0.0030	0.005	0.0071	0.027
			73	11	[0.58]	[0.76]	[0.62]	[0.73]	[0.68]
5-Fluorouracil	801	Fluorouracil	186		0.22	0.70	0.79	0.82	0.35
			129	57	[0.54]	[0.48]	[0.46]	[0.46]	[0.52]
Gemcitabine	752	Gemcitabine	156		0.25	0.015	0.0052	0.029	0.0057
			75	81	[0.53]	[0.60]	[0.62]	[0.59]	[0.62]
Irinotecan	796	Irinotecan	25		0.81	0.39	0.757	0.54	0.46
			7	18	[0.39]	[0.54]	[0.41]	[0.49]	[0.52]
Oxaliplatin	724	Oxaliplatin	66		0.38	0.017	0.0059	0.028	0.035
			43	23	[0.52]	[0.66]	[0.69]	[0.64]	[0.64]
Paclitaxel	753	Paclitaxel	160		0.032	0.026	0.28	0.10	0.0042
			111	49	[0.59]	[0.60]	[0.53]	[0.56]	[0.63]
Pemetrexed	898	Pemetrexed	38		0.16	0.38	0.56	0.16	0.367
			18	20	[0.60]	[0.53]	[0.49]	[0.59]	[0.53]
Temozolomide	746	Temozolomide	96		0.56	0.34	0.51	0.59	0.19
			11	85	[0.49]	[0.54]	[0.50]	[0.48]	[0.58]
Vinorelbine	746	Vinorelbine	30		0.31	0.048	0.053	0.19	0.35
			23	7	[0.57]	[0.71]	[0.71]	[0.61]	[0.55]

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. Samples were divided in two categories: Responders and Nonresponders (NR) (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.