Finding Transcription Factor Binding Motifs for Coregulated Genes by Combining Sequence Overrepresentation with Cross-Species Conservation

Figure 2

Average relative entropy of the motifs. We choose the 100 sequences found in the upstream of Ace2-regulated S. cerevisiae genes with the smallest overrepresentation P-values and compute their average relative entropies in the multiple alignments of orthologous upstream sequences of the four related species. The results were displayed with a scatter plot of P-value versus average relative entropy. The arrow points to the known binding motif GCTGGT of Ace2 in S. cerevisiae. The average relative entropy of the known binding motif is greater than that of most other sequences.