Table 4. Model evaluation by logical steady state and microarray analysis.

Experiment source scenario	Experiment target scenario	Model LSSA simulation	Total number of genes	Number of true predictions	p-value of true predictions	Number of small error predictions	Number of large error predictions
U2OS cells under DNA damage	SAOS2 cells under DNA damage	P53 wt with DNA damage ON vs p53 null with DNA damage ON	200	109(54.5%)	2.6×10−10	80(40%)	11(5.5%)
U2OS cells without DNA damage	SAOS2 cells without DNA damage	P53 wt with DNA damage OFF vs p53 null with DNA damage OFF	200	111(55.5%)	4.1×10−11	77(38.5%)	12(6%)
U2OS cells without DNA damage	U2OS cells under DNA damage	P53 wt with DNA damage ON vs p53 wtwith DNA damage OFF	200	142(71%)	<<10−15	56(28%)	2(1%)
SAOS2 cells without DNA damage	SAOS2 cells under DNA damage	P53 null with DNA damage ON vs p53 null with DNA damage OFF	200	131(65.5%)	<<10−15	65(32.5%)	4(2%)
HCT116 cells p53+/+ without DNA damage	HCT116 cells p53−/−without DNA damage	P53 null with DNA damage OFF vs p53 wt with DNA damage OFF	169	88(52.1%)	1.8×10−7	72(42.6%)	9(5.3%)

The changes of gene expression in experimental microarray data were compared with model simulation results. The number of true predictions, small errors, large errors and their percentage were calculated and listed.