Table 3.

Evaluation of the induced rules using annotations from the three parts of Gene Ontology

	Gene Ontology evaluation (significant fractions P < 0.01)
	Rule (P-values)			Random tests Similar expression/common motifs/random
Expression data	Molecular function	Biological process	Cellular component	Molecular function			Biological process			Cellular component
Cell cycle	0.31 (0.000)	0.46 (0.000)	0.41 (0.000)	0.05	0.04	0.01	0.13	0.18	0.03	0.03	0.04	0.00
Sporulation	0.26 (0.000)	0.54 (0.000)	0.44 (0.000)	0.08	0.04	0.01	0.19	0.17	0.02	0.05	0.03	0.00
Diauxic shift	0.30 (0.000)	0.43 (0.000)	0.44 (0.000)	0.04	0.05	0.02	0.11	0.17	0.03	0.02	0.03	0.00
Heat and cold shock	0.54 (0.000)	0.64 (0.006)	0.60 (0.000)	0.24	0.06	0.03	0.46	0.24	0.05	0.17	0.04	0.01
Pheromone	0.51 (0.000)	0.67 (0.000)	0.60 (0.000)	0.10	0.05	0.01	0.25	0.16	0.02	0.08	0.03	0.00
DNA-damaging agents	0.39 (0.000)	0.64 (0.000)	0.61 (0.000)	0.09	0.05	0.01	0.19	0.17	0.03	0.07	0.04	0.00

A rule is said to be significant if at least one Gene Ontology term used to annotate the matching genes obtained a Bonferroni-corrected P-value of <0.01. The table gives the fraction of significant rules for each data set and each part of Gene Ontology, and compares these values to what is observed when randomly selecting corresponding sets of genes with only similar expression, common binding sites, or neither. All three random tests produce a P-value that is the probability of observing a higher value than the one reported for the rules. We show the highest of these P-values in parentheses and mark the corresponding random test in bold if this P-value is >0. Additional statistics on the standard deviation of the random tests may be found at our Web site.