Table 1. Genes with significant copy number changes and the number of their correlated genes.

Gene symbol	RefSeq accession	Entrez ID	Cytoband	Copy number status	Pearson r	P valuea	Spearman r	P valueb	Number of in trans correlated genes	P valuec
CCNE1	NM_001238.2	898	19q12	Amplification	0.48	<0.001	0.34	<0.001	300	0.03
CDKN2B	NM_004936.3	1030	9p21	Deletion	0.72	<0.001	0.70	<0.001	7	0.28
CDKN2A	NM_000077.4	1029	9p21	Deletion	0.77	<0.001	0.77	<0.001	14	0.32
MUC1	NM_001018016.2	4582	1q21	Amplification	0.10	0.05	0.12	0.02	2	0.42
MYC	NM_002467.4	4609	8q24.21	Amplification	0.25	<0.001	0.20	<0.001	14	0.45
CCND1	NM_053056.2	595	11q13	Amplification	0.49	<0.001	0.34	<0.001	446	0.46
E2F3	NM_001243076.2	1871	6p22	Amplification	0.83	<0.001	0.66	<0.001	105	0.61
CREBBP	NM_001079846.1	1387	16p13.3	Deletion	0.53	<0.001	0.48	<0.001	4097	0.73
ERBB2	NM_001005862.2	2064	17q12	Amplification	0.62	<0.001	0.38	<0.001	1850	0.79
TP53	NM_000546.5	7157	17p13.1	Deletion	0.29	<0.001	0.34	<0.001	2122	0.81
MDM2	NM_001145337.2	4193	12q14.3-q15	Amplification	0.76	<0.001	0.52	<0.001	9	0.88
CEBPA	NM_001285829.1	1050	19q13.1	Amplification	0.16	0.001	0.24	<0.001	624	0.92
RB1	NM_000321.2	5925	13q14.2	Deletion	0.52	<0.001	0.46	<0.001	1580	0.93
TRIO	NM_007118.2	7204	5p15.2	Amplification	0.47	<0.001	0.49	<0.001	4035	0.99

^aP values were obtained by Pearson correlation test between copy number values and gene expression levels.

^bP values were obtained by Spearman correlation test between copy number values and gene expression levels.

^cP values were obtained by log-rank test.