Fig. 5

Klf9 peaks group into shape clusters that show different likelihood of association with repressed genes, and degree of transcriptional repression. a Klf9 peaks in HT22 cells can be grouped into three clusters based on shape and height characteristics. Example peaks from each cluster are shown. The graph height (200 pixels on UCSC genome browser) and viewing window size (2 kb) are held constant. b Distribution of the Klf9 consensus motif (top) and mapped sequencing read density (bottom) within peaks from each shape cluster. Sequencing read density closely tracks the probability of the occurrence of consensus motifs in all clusters. c Average number of Sp/Klf motifs and number of Klf9 consensus motifs present in peaks belonging to each cluster. Boxplots indicate 75% and 25% quantiles; dots indicate 5% and 95% quantiles. Means with the same letter are not significantly different (p < .05; Kruskal-Wallis non-parametric ANOVA). Top: peaks of clusters 2 and 3 contain more Sp/Klf-like motifs than those of cluster 1; bottom: peaks of cluster 3 have more copies of the Klf9 consensus motif than peaks of clusters 1 and 2. d Percentage of peaks of each cluster associated with repressed genes. e Median ratio of mRNA levels in HT22 [TR/TO-Klf9] cells treated +/− dox of genes associated with peaks from each cluster. Means with the same letter are not significantly different (p < .001; Kruskal-Wallis non-parametric ANOVA)