Table 2 (EXTENDED). Evaluation of the induced rules using the binding data from Lee et al. (2002) and Harbison et al (2004). A rule is said to be significant if at least one transcription factor binding any of the matching genes obtained a Bonferroni corrected P-value less than 0.01 (only bindings at P < 0.01 from Lee et al. (2002) were considered). The table gives the fraction of significant rules for each dataset, and compares these values to what is observed when randomly selecting corresponding sets of genes with only similar expression, common binding sites or neither. The P-value given for each dataset is the highest probability of observing a higher value than the one observed for the rules in any of the random tests (in fact all three tests produce one P-value each, but only the highest P-value is shown and indicated in bold). The table also gives the Euclidean distance threshold (normalized with a number of measurement points) used to define similar expression profiles and the number of rules induced for each expression dataset.

Expression data

Expression

similarity

thresholds

No. rules unique/all

Binding data evaluation (significant fractions P < 0.01)

Lee et al./Harbison et al.

Rules

(P-value)

Random tests (std. dev.)

Similar expression

Common motifs

Random

Cell cycle

0.250

39/109

0.538/0.487 (0.000)

0.109 (0.049)

0.171 (0.062)

0.019 (0.020)

Sporulation

0.250

45/81

0.133/0.178 (0.708)

0.085 (0.041)

0.179 (0.057)

0.015 (0.018)

Diauxic

shift

0.200

150/428

0.291/0.315 (0.000)

0.061 (0.029)

0.183 (0.029)

0.016 (0.010)

Heat and

cold shock

0.125

52/123

0.520/0.529 (0.000)

0.180 (0.053)

0.175 (0.053)

0.017 (0.018)

Pheromone

0.150

53/91

0.388/0.365 (0.001)

0.135 (0.048)

0.170 (0.055)

0.017 (0.018)

DNA-damaging

agents

0.200

59/116

0.351/0.345 (0.000)

0.101 (0.040)

0.165 (0.049)

0.018 (0.018)