Table 2.

Putative key molecules that regulate DEPs at 3, 24, 48, and 96 h during ATRA-induced differentiation of HL-60 cells.

Time Point	Key Molecule Name	Reached from TF Set 1	Reachable Total 2	Score 3	FDR 4	Z-Score 5	Ranks Sum 6
Combined 3-24-48-96 h	YY1	22	32835	0.650	0.013	2.779	59
	plk1{p}	22	32762	0.640	0.002	2.803	63
	PARP1	22	32360	0.607	0.006	2.950	63
	faim	22	32361	0.607	0.006	2.950	64
	MKK6	22	33716	0.721	0.004	2.325	88
	NR1B1 (RARA)	22	30223	0.505	0.018	3.007	204

¹ “Reached from TF set”—the number of the TFs from the input set (Supplemental Table S7) that is reached from the respective key molecule; ² “Reachable total”—the total number of molecules that can be reached from the key molecule, independent of the input set; ³ “Score”—the value reflecting how well the respective key molecule is connected with other molecules in the database, and how many molecules from the input set are present in the network triggered by this key molecule, the higher value—the better suitability (threshold value > 0.2); ⁴ FDR—false discovery rate (from 1000 random input sets); ⁵ “Z-score”—the value that reflects how specific each key molecule is for the input list, the higher value—the better suitability (threshold value > 1); ⁶ “Rank sum”—composite value that reflects the impact of Score and Z-score simultaneously, the lower value—the better suitability.