Table 1. Integration of RNAseq, ChIPseq and TCGA data.

Cell line	Gene	RNAseq (siNKX2-1/siNTC)	ChIPseq peak rank	TCGA FDR a (%)
H1819	EGFR	0.349	84	5.4
	EFR3B	0.716	123	1.1
H661	EGFR	0.397	1638	5.4
	PAX9	0.632	1400	0.3
	MRPL42	0.644	1922	0.3
	TSEN15	0.644	2163	3.0
	RAI14	0.649	1989	9.2
	MAP2K6	0.667	2523	0.3
	LOC654342	0.696	2906	3.6
	GNG4	0.696	1070	5.4
	MED30	0.714	1551	0.8
	RALA	0.722	3122	1.1
	MCTP1	0.733	261	7.8
	ARL4A	0.750	401	9.2
HCC1195	CCL20	0.465	908	7.8
	CNGA3	0.478	1542	7.8
	EGFR	0.568	1388	5.4
	TREM1	0.571	1350	6.4
	MMP13	0.573	1367	9.2
	ETV5	0.600	437	6.4
	PENK	0.677	1564	9.2
	IL1RAP	0.683	1330	5.4
	NKX2-8	0.691	978	2.6
	ABCA4	0.691	328	5.4
	NAMPT	0.709	1176	1.5
	HMGA2	0.712	1148	4.4
	ASPHD2	0.714	1199	1.5
	C5orf4	0.739	347	9.2
	EFR3B	0.744	537	1.1
	LPIN1	0.745	698	5.4
	FAM101A	0.750	275	1.1
HCC1833	NGF	0.513	7	4.4
	CCDC14	0.622	202	0.3
	HMP19	0.654	216	7.8
	HMGA2	0.676	193	4.4
	BCL2	0.706	95	0.6
	ESPL1	0.741	184	0.0

^aAmplified/highly-expressed vs. non-amplified/highly-expressed (FDR<10%)