Table 1.

Example of an induced rule: a rule combining binding sites RAP1, SWI5, and MCM1′

RULE: IF RAP1 and SWI5 and MCM1′ THEN similar expression in cell cycle, sporulation, diauxic shift, heat and cold shock, and DNA-damaging agents (see Fig. 2)
Gene symbol	Biological process	Molecular function	Cellular component	Possible transcription factors (P < 0.01)
RPL16B	Protein biosynthesis	RNA binding, structural constituent of ribosome	Cytosolic ribosome (sensu Eukarya), large ribosomal subunit	FHL1, GAT3, PDR1, RAP1, RGM1, YAP5
RPL26A	Protein biosynthesis	RNA binding, structural constituent of ribosome	Cytosolic ribosome (sensu Eukarya), large ribosomal subunit	FHL1, RAP1
RPS18A	Protein biosynthesis	Structural constituent of ribosome	Cytosolic ribosome (sensu Eukarya), eukaryotic 43S pre-initiation complex, eukaryotic 48S initiation complex, mall ribosomal subunit	FHL1, GAT3, HIR2, RAP1, RGM1, YAP5
RPL30	Protein biosynthesis, rRNA processing, mRNA splicing, regulation of translation	Structural constituent of ribosome	Cytosolic ribosome (sensu Eukarya), cytoplasm, large ribosomal subunit	FHL1, GAT3, RAP1, SFP1
RPL18A	Protein biosynthesis	Structural constituent of ribosome	Cytosolic ribosome (sensu Eukarya), large ribosomal subunit	FHL1, MAL13, RAP1, YAP5
RPL14A	Protein biosynthesis	RNA binding, structural constituent of ribosome	Cytosolic ribosome (sensu Eukarya), large ribosomal subunit	FHL1, GAT3, GRF10(Pho2), GTS1, RAP1
SST2	Signal transduction, adaptation to pheromone during conjugation with cellular fusion	GTPase activator activity	Plasma membrane	DIG1, FHL1, RAP1, STE12
RPS24A	Protein biosynthesis	Structural constituent of ribosome	Cytosolic ribosome (sensu Eukarya), eukaryotic 43S pre-initiation complex, eukaryotic 48S initiation complex, small ribosomal subunit	FHL1, GAT3, PDR1, RAP1, RGM1, SMP1, YAP5

The rule was found in five of the six gene expression data sets. All genes containing the three binding sites in their promoter regions are listed in the table together with their annotations as to the Gene Ontology biological process, molecular function, and cellular component, and the transcription factors they bind according to Lee et al. (2002) (P-value < 0.01). The gene expression profiles for all genes in this table are shown in Figure 2. All the induced rules and their evaluation with Gene Ontology and binding data can be found at our Web site.