Figure 3. All predicted DNA and RNA motifs for the yeast gene clustering partition.

Columns correspond to gene clusters and rows correspond to predicted motifs arranged into putative functional modules. For each cluster, the most significant GO enrichment is shown at the top. The yellow color-map indicates over-representation of a motif in a given cluster; significant over-representation (p<0.05 after Bonferroni correction) is highlighted using red frames. Similarly, the blue color-map and blue frames indicate under-representation. For each motif, we indicate 1) location, i.e., 5′ upstream region or 3′UTR, 2) mutual information (MI) value, 3) Z-score associated with the MI value, calculated using 10,000 randomization tests, 4) robustness score ranging from 0/10 to 10/10 obtained from 10 jack-knife trials of randomly removing 1/3 of the genes and reassessing the statistical significance of the resulting MI values, 5) position bias indicator (“Y” if a position bias is observed), 6) orientation bias indicator, 7) conservation index, 8) seed that gave rise to the motif, and 9) name of the closest known motif in our motif database (with CompareACE score > 0.8). For more details, see the Supplementary Methods section about FIRE p-value heat-maps.