Table 1. Differentially expressed BCL-2 genes in breast cancer subtypes.

The logFC is indicated in the table, all the results refer to an FDR < 0.05. Empty lines indicate that the gene is not differentially expressed in the corresponding comparison. BCL2A1 results the only pro-survival BCL-2 gene which is up-regulated in the majority of the comparisons. We notice that one of the main pro-survival genes, i.e. BCL-2 is mostly down-regulated in the TCGA-BRCA samples with HER2 and Basal subtypes. We do not report the comparison between LumA and LumB since none of the BCL-2 family members is deregulated in this comparison.

GENE	Cancer vs Normal	Basal vs HER2	Basal vs LumA	Basal vs LumB	Basal vs Normal	HER2 vs LumA	HER2 vs LumB	HER2 vs Normal	LumA vs Normal	LumB vs Normal
BCL-2			-2.35	-1.91	-2.20	-2.26	-1.82	-2.11
BCL2A1	1.31	1.25	2.02	1.61	2.77			1.51		1.15
BCL2L1
BCL2L2	-1.01				-1.17			-1.21
BCL2L10
MCL-1
BAK1					1.34			1.03
BAX
BOX					-1.46			-1.47	-1.06