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. 2016 Nov 28;45(4):1743–1759. doi: 10.1093/nar/gkw1156

Figure 3.

Figure 3.

Cluster analysis of temporal H3K4me3 occupancy at promoter sites. (A) All promoter sites with differential levels of H3K4me3 in control relative to KDM5 KD cells at one or more of the analyzed time points were clustered based on the temporal profile of H3K4me3 during the early stage of adipocyte differentiation (day 0 to 2) in control cells. (B) H3K4me3 promoter signal in the six clusters shown in A in control (blue) and KDM5 KD (red) cells at day 0. The colored region illustrates the 95% confidence interval around the median (dashed line) as determined by bootstrapping. (C) Expression signal based on RNA-seq of genes assigned to the promoters from the six different clusters shown in A in control (blue) and KDM5 KD (red) cells at day 0. The colored region is the 95% confidence interval around the median (dashed line) as determined by bootstrapping. The number of genes in C differs from the number of promoter sites in A-B due to a subset of the cluster promoter sites being associated with genes not expressed at detectable levels in 3T3-L1 cells, which were therefore excluded from the analysis. B and C: P-value: # P <0.05, ## P <2.2e-8, and ### P <2.2e-16, control compared with KDM5 KD, Wilcoxon rank sum test.