TABLE 2.

The location and average copy numbers the 33 signature genes

Rank	Gene	Location	Category	TCGA Tumors			TCGA on-malignant		Spore Tumors		EDRN/Canary Tumors
				LUAD	LUSC	P-value	LUAD	LUSC	LUAD	LUSC
1	SPATA16	3q26.31	A	2.09	3.31	3.1E-77	2.01	2.01	2.08	3.38	1.98
2	USP13	3q26.2-q26.3	A	2.07	3.36	6.32E-76	2.01	2.01	2.20	3.54	1.99
3	TPRG1	3q28	A	2.05	3.09	7.29E-85	2.01	2.01	2.17	3.51	1.96
4	ZMAT3	3q26.32	A	2.07	3.39	6.76E-73	2.00	2.01	2.20	3.54	2.00
5	MFN1	3q26.33	A	2.07	3.36	9.98E-74	2.01	2.01	2.20	3.54	2.00
6	HTR3D	3q27.1	A	2.07	3.45	8.75E-67	2.01	2.01	2.14	3.36	2.01
7	ABCF3	3q27.1	A	2.06	3.40	1.34E-71	2.01	2.01	2.14	3.36	2.03
8	ABCC5	3q27	A	2.06	3.45	1.86E-66	2.01	2.01	2.14	3.36	2.01
9	VWA5B2	3q27.1	A	2.06	3.38	1.19E-72	2.01	2.01	2.18	3.53	2.11
10	FLJ42393	3q27.3	A	2.05	3.14	1.58E-81	2.01	2.02	2.17	3.51	2.02
11	ADIPOQ	3q27	A	2.05	3.17	4.87E-80	2.01	2.01	2.17	3.51	2.00
12	RTP2	3q27.3	A	2.05	3.14	4.58E-81	2.01	2.01	2.17	3.51	1.99
13	SST	3q28	A	2.05	3.14	4.58E-81	2.01	2.01	2.17	3.51	1.99
14	YEATS2	3q27.1	A	2.06	3.49	5.64E-59	2.01	2.01	2.18	3.53	2.01
15	LOC100131635	3q27.3	A	2.05	3.14	6.37E-81	2.01	2.01	2.17	3.51	1.97
16	PPP1R2	3q29	A	2.06	3.08	2.35E-85	2.01	2.01	1.93	2.90	2.06
17	OSTN	3q28	A	2.05	3.09	2.14E-83	2.01	2.02	2.17	3.51	1.99
18	SERPINI2	3q26.1	A	2.11	3.20	8.5E-78	2.01	2.01	2.08	3.49	1.98
19	PDCD10	3q26.1	A	2.11	3.20	3.22E-77	2.01	2.01	2.08	3.49	1.98
20	PIK3CA	3q26.3	A&B	2.07	3.17	1.55E-78	2.01	2.01	2.20	3.54	1.98
21	SOX2	3q26.3-q27	B	2.07	3.45	7.48E-57	2.01	2.01	2.24	3.65	2.02
22	STIM2	4p15.2	A	2.04	1.79	3.12E-25	2.01	2.01	1.96	1.66	2.08
23	TBC1D19	4p15.2	A	2.04	1.79	3.83E-25	2.01	2.01	2.0	1.85	2.08
24	RBPJ	4p15.2	A	2.04	1.80	4.34E-18	2.01	2.02	1.98	1.75	2.08
25	C6orf203	6q21	A	1.83	2.07	1.15E-06	2.01	2.01	1.88	2.12	1.87
26	HACE1	6q16.3	A	1.82	2.06	1.32E-06	2.01	2.02	1.86	2.10	1.86
27	BVES	6q21	A	1.82	2.07	1.24E-06	2.01	2.01	1.88	2.12	1.86
28	ALKBH7	19p13.3	A	1.81	1.95	4.88E-18	2.01	2.01	1.87	1.95	2.18
29	C9orf53	9p21.3	A	1.75	1.59	7.27E-08	2.01	2.01	1.79	1.67	2.04
30	CLPP	19p13.3	A	1.81	1.95	4.88E-18	2.01	2.01	1.87	1.95	2.18
31	MIR1233-2	15q14	A	1.80	1.95	5.25E-12	1.94	1.97	2.33	2.30	1.88
32	NKX2-6	8p21.2	A	1.81	1.74	0.10E-03	2.01	2.01	1.85	1.69	1.92
33	SIGLEC14	19q13.32	A	1.80	1.94	5.04E-06	1.88	1.90	1.91	2.13	2.19

• Rank: ranked by the coefficients to the classification model. P-value is obtained by the two-tailed t-test between copy numbers of LUADs and LUSCs.

• There are no LUSC samples in EDRN/Canary dataset.

• For convenience, CNVs of TCGA dataset were transformed back to the regular copy number format (2 × 2^CNV).

• Category A: Genes selected by multivariate classification methods; Category B: Proved tumor associated genes for lung cancer;