Table 1.

ChIP-on-chip sites in the test set predicted to be p53 binding sites by the sequence-only and combined-evidence models

Model	Large set	Intermediate set	Stringent set
Combined-evidence	330 (42.47 %)	147 (18.92 %)	35 (4.50 %)
Sequence-only	307 (39.51 %)	93 (11.97 %)	14 (1.80 %)

Among the 1545 ChIP-on-chip sites (26), 777 were used as a test set. Counts are given with percentages in parentheses. The fraction of sites predicted by the two models was significantly different for the intermediate (exact binomial test, P = 2.62 × 10⁻⁸) and stringent (exact binomial test, P = 2.01 × 10⁻⁶) sets.