Table 3 Shown are the functional validation results for 21 TFs enriched (at FDR ≤0.1 and P-value ≤0.05) for either taxane, paclitaxel (PAX) or docetaxel (DOC)

Number	TF	GENMi enrichments				Cell lines
		PAX		DOC		BTF549		MDA-MB-231
		P-value	FDR	P-value	FDR	PAX	DOC	PAX	DOC
1	BATF	0.0142	0.07	0.5160	1.00			UP	UP
2	BCL3	0.4112	0.56	0.0020	0.03	UP	UP	UP	UP
3	BHLHE40	0.0088	0.06	0.0487	0.30			UP	UP
4	CEBPB	0.0024	0.02	0.3199	0.86	UP	UP	UP	UP
5	ELF1	0.0020	0.03	0.0147	0.20	UP	UP	UP	UP
6	FOS	0.0127	0.09	0.2007	0.63			UP	UP
7	FOSL2	0.0285	0.12	0.0012	0.03			UP	UP
8	FOXM1	0.2754	0.44	0.0052	0.07		UP	UP	UP
9	IKZF1	0.0213	0.09	0.1422	0.78			UP	UP
10	KDM5B	0.0016	0.02	0.0004	0.04			UP	UP
11	MAFK	0.0016	0.02	0.6006	1.00	UP	UP	UP	UP
12	MTA3	0.0027	0.03	0.1556	0.62		UP	UP	UP
13	NFIC	0.0020	0.02	0.0131	0.18	UP	UP	UP	UP
14	RBBP5	0.0012	0.02	0.3613	0.69				UP
15	REST	0.0008	0.04	0.2343	0.57	UP	UP	UP	UP
16	SIN3A	0.0028	0.03	0.5193	0.78				UP
17	TBL1XR1	0.0071	0.04	0.5347	1.00
18	TCF7L2	0.0056	0.04	0.1004	0.45				UP
19	WRNIP1	0.0004	0.02	0.2273	0.59		UP	UP	UP
20	ZBTB33	0.0044	0.05	0.9282	0.95			UP	UP
21	ZNF263	0.0168	0.09	0.0255	0.26			UP	UP

Abbreviations: FDR, false discovery rate; GENMi, Gene Expression iN the Middle; TF, transcription factor.
Validation was performed in two triple-negative breast cancer cell lines (BTF549 and MDA-MB-231). For each cell line, drug and TF, a small interfering RNA (siRNA) knockdown experiment was performed, followed by an MTA assay for the drug. Comparisons were made to negative siRNA experiments to determine whether the TF decreased, increased or did not affect the sensitivity of the cell to the drug. ‘UP’ in the table refers to decreased sensitivity or desensitization of the cell to the drug, that is, the TF knockdown increased cell resistance/survivability to increasing concentrations of the apoptotic drug. In no case was the knockdown found to decrease cell resistance. Cells with P-value ≤0.05 or FDR ≤ 0.1 are colored gray, and represent the drug (PAX or DOC or both) for which the TF was predicted to influence response.

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