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Table 5.

Study Set Results at Different P Values[i]

Quantile		Number of motif predictions		Motif predictions with avg MAP ≥ critical value	Correspondence with known sites for:
Quantile		Number of motif predictions		Motif predictions with avg MAP ≥ critical value	Motif predictions with avg MAP ≥ critical value	Motif predictions with avg MAP < critical value
80% (P = 0.20)	163	129	93	19
90% (P = 0.10)	163	108	81	31
95% (P = 0.05)	163	85	64	48
99% (P = 0.01)	163	50	37	75

[i] Using orthologous data sets containingEscherichia coli–Salmonella typhi–Yersinia pestis–Vibrio cholerae–Haemophilus influenzae–Shewanella oneidensis–Pseudomonas aeruginosa and analyzing motif predictions that contain sites from at least two species.