Figure 9

Motif and position distribution detected in the down-regulated clusters. The top 100 clusters having the highest log concentration and down-regulated (i.e., the HeLa cells expressed higher levels than the THP-1 cells) at the top and bottom peaks were used for motif discovery analysis. (A) We found differentially abundant motifs by Dispom [20], and we compared standard motif representations in the JASPAR core database [21] using the Tomtom program [22]. The sequence logo and the corresponding consensus sequence at the left-hand side were predicted from the clusters at the top peaks, and the right-hand side shows the result at the bottom peaks. The sequence logos at the top left and right sides show the KLF4 motif, and the ones below this are obtained through predictions. For the consensus sequences, B stands for C, G, or T, K stands for G or T, and R stands for A or G. (B) Histograms of the predicted positions relative to TSSs of the motifs at each cluster. As well as (A), the figure at the left side shows the result at the top peaks, and right side is the plot at the bottom peaks.