Table 4. DEGs identified using DESeq2 and UQ-pgQ2.

The DEGs from 17,584 protein coding genes are determined given a nominal FDR ≤0.05 and an optimal |logFC| cutoff in Table 3.

Data	Normalization	DEGs	Up	Down
TNBC	UQ.pgQ2	1,584	949	635
	DESeq2	1,913	1099	814
	Common DEGs	1,546	915	631
ER+HER2-BC	UQ.pgQ2	2,303	1,161	1,142
	DESeq2	2,649	1,195	1,454
	Common DEGs	2,212	1,074	1,138