Table 2.

Test results of PAP using coregulated gene sets collected from the literature

Gene cluster	TF	Matrix	〈R-score 〉	Rank	P-value
Muscle specific^a	SRF	M00810	4.605	1	∼0
	MEF	M00405	2.976	2	∼0
	Myf	M00001	2.976	1	∼0
	SP1	MA0079	2.386	31	0.007
Liver specific^b	HNF-1	M00790	3.561	1	∼0
	HNF-3	M00791	2.406	3	0.002
	C/EBP	M00116	2.242	4	0.0095
	HNF-4	M00134	2.192	6	0.0036
Heat shock response^c	HSF2	M00147	2.477	1	0.0033
	HSF1	M00146	2.375	2	0.0048
PTH-regulated^d	CREB	M00801	3.73	2	∼0
	AML1	M00751	3.27	6	0.0001
	AP-1	M00173	2.564	77	0.0069
NF-κB immune genes^e	NF-κB	M00774	2.882	2	∼0

Eight gene clusters that are regulated by common transcription factors were collected from the literature. For each TF, the 〈R-score 〉 was calculated as described in Results, and the rank of the true TF amongst all of the characterized TFs was determined. PAP predicted the true TF within the top six in 12 test cases. Low P-values indicate that the predictions are statistically significant.
↵a Wasserman et al. 2000.
↵b Krivan and Wasserman 2001.
↵c Visala Rao et al. 2003.
↵d Qiu et al. 2003.
↵e Baeuerle and Baichwal 1997.

A systematic model to predict transcriptional regulatory mechanisms based on overrepresentation of transcription factor binding profiles