Table 2.

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

Gene cluster
TF
Matrix
〈R-score 〉
Rank
P-value
Muscle specifica 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 specificb 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 responsec HSF2 M00147 2.477 1 0.0033
HSF1 M00146 2.375 2 0.0048
PTH-regulatedd CREB M00801 3.73 2 ∼0
AML1 M00751 3.27 6 0.0001
AP-1 M00173 2.564 77 0.0069
NF-κB immune genese
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.