iGC—an integrated analysis package of gene expression and copy number alteration

BMC Bioinformatics

Table 2 The top three significant genes with copy number gain or loss in the TCGA dataset

Genes	GE mean gain	GE mean loss	GE mean neutral	GE mean diff.	CNA prop. gain	CNA prop. loss	t-test	FDR^a
GNPAT (G)	0.372	−1.048	−0.200	0.601	0.558	0.015	3.01E-61	3.43E-58
SETDB1 (G)	0.505	NA	−0.056	0.562	0.556	0	4.55E-58	2.60E-55
ANGEL2 (G)	0.588	−0.664	0.032	0.577	0.549	0.013	1.30E-55	4.93E-53
GSTM1 (L)	0.588	−0.961	0.026	−1.281	0.310	0.409	1.02E-33	5.10E-31
TOX (L)	−2.599	−3.237	−2.455	−0.777	0.023	0.337	1.64E-19	4.10E-17
LYN (L)	0.224	−0.134	0.279	−0.410	0.034	0.314	4.16E-19	6.92E-17

GE gene expression, CNA copy number alteration, Diff difference, Prop proportion, FDR false discovery rate, NA not available
^aGenes were ordered based on the FDR values

ISSN: 1471-2105