Table 1. Correlation between PWM scores and expression
OrganismExperimentBiological process/tissueMotifAverage information content%RIVP‐value
YeastMicroarrayCell cycle (G2)Mcm10.594.93.4 × 10−9
HumanMicroarrayLiverHNF‐10.622.21.6 × 10−6
HumanMicroarrayPancreasC/EBP beta0.762.52.5 × 10−7
HumanMicroarrayCell cycle (G1/S)E2F1.745.91.7 × 10−12
MouseMicroarrayLiverHNF‐10.622.12.1 × 10−6
MouseMicroarrayLiverHNF‐40.602.04.1 × 10−6
HumanChIP‐chipLiver/HNF‐1HNF‐10.6214.78.7 × 10−37
  • Comparison of percent reduction in variances (%RIVs) between yeast and mammals is shown. Single linear splines were used to obtain the %RIV. Yeast cell‐cycle data were obtained from Spellman et al (1998), liver and pancreas microarray data from Su et al (2004), liver ChIP‐chip data for HNF‐1 from Odom et al (2004) and human cell‐cycle data from Whitfield et al (2002). Mcm1 matrix was obtained from Bussemaker et al (2001); all other matrices were obtained from TRANSFAC and JASPAR databases. P‐values were calculated using an F‐test (see Materials and methods). Average information content refers to the information content of the position weight matrix, averaged over all the positions (columns). It is 2.0 for non‐degenerate words and 0 if all positions were N's (see Materials and methods).