Table 2.

Significant positively (and negatively) selected genes and pathways that have experimental support in different comparisons

Dataset	Comparisons	Direction	Genes or pathways	FDR	Rank	Experimental support
Leukemia	HL-60, KBM7, treatment versus control	Positive	MAP4K3	0.14	9	[22]
			EPM2A	0.14	10	[23]
		Negative	KEGG: ribosome	4.71E-4	1/181	[3]
	HL-60 versus KBM7	Negative	IGF1R	1.98E-3	1	[30]
	KBM7 versus HL-60	Negative	BCR	1.60E-3	7	[31]
			ABL1	1.98E-3	18
			KEGG: chronic myeloid leukemia	9.00E-4	6/181
Melanoma	PLX treatment versus control (14 days)	Positive	CDH13	0.017	9	[20,21]
			PPT1	0.085	14	[19]
			NF1, NF2, MED12, CUL3, TADA1, TADA2B	<0.031	11 (max)	[4]
		Negative	RREB1	0.050	1	[25,26]
	PLX treatment versus control (7 days)	Positive	NF1, NF2, MED12, CUL3, TADA1, TADA2B	<0.030	26 (max)	[4]
		Negative	EGFR	0.025	6	[28,29]
			REACTOME: SHC1 events in EGFR signaling	0.069	1/676
			REACTOME: signaling by constitutive active EGFR	0.069	2/676
	DMSO treatment 14 days versus 7 days	Negative	KEGG: oxidative phosphorylation	3.30E-3	2/181	[18]
ESC	ESC versus plasmid	Positive	TRP53	0.010	1	[24]
		Negative	KEGG: ribosome	2.83E-4	1/181	[6]
			NANOG, POU5F1, RAD51, BRCA1	<0.016	217 (max)

For other top ranked genes, see Tables S3 to S10 in Additional file 2 and Tables S10 to S18 in Additional file 3.