Figure 5.

Clustering of genes based on their changes in RNAPII occupancy during differentiation reveals five distinct clusters. RNAPII ChIP-seq was performed during differentiation, and the relative overall occupancy in the genes was calculated as described using Log₂ ratios of RNAPII occupancy at each day relative to day 0. (A) Genes with regulated RNAPII binding were separated into five distinct clusters using the k-means algorithm with squared Euclidean distance. (B) The clustered genes were assigned to biological function based on GO using the web tool DAVID. The total number of genes within a given cluster that belongs to a particular GO category as well as the P-value for the category is indicated (RNAPII). The number of genes with associated PPARγ:RXR target sites is listed with the corresponding P-values (PPARγ:RXR RNAPII). Significance level: P < 0.05; (NS) not significant.