Figure 3

Limited retention of mouse PPARγ and C/EBPα binding sites. (A) Bar diagrams representing the fraction of retained C/EBPα sites (blue), retained PPARγ binding sites (red), and lost binding sites (gray), all from mouse to human using the binary method. (B) Retention using the enrichment method. The plot shows the distribution of tag enrichment in the human regions orthologous to the mouse sites, calculated as log₂(fold change compared to random expectation). High values indicate high levels of enrichment and therefore retention. C/EBPα and PPARγ retention is indicated by blue and red color, respectively. The distributions are shown as a variant of boxplots called "violin plots", a rotated density plot. The width of the colored area corresponds to how many data points that fall into that range [48]. The black dot within each plot represents the median and hinges the 75^th, and 25^th quartiles of the respective distribution, similar to a box plot. In both cases most of the probability density is located around a log fold change of 0, indicating that most regions are not retained. (C) Example of retention of multiple mouse/human sites in the PPARG2 locus. The ChIP-seq density is shown for PPARγ (red) and C/EBPα (blue) in both species, together with the UCSC gene models. The PPARG2 locus with TSS and exons is indicated as a black line and filled bars, respectively. Grey lines show center in mouse sites and corresponding regions in human. Green and pink arrow structures represent alignment blocks from the UCSC browser.