Figure 4

Applying ngs.plot to the study of Tet1 in mESC P19.6 cells during differentiation. All heatmaps are resized to match each other’s height for display purposes. A. Tet1 and 5hmC enrichment at different functional regions – CGIs at proximal promoters, canonical exons, and enhancers, including 3 Kb flanking regions. All regions are ranked by the “total” algorithm. “L” – 5’ left, “R” – 3’ right as defined by the gene that includes the CGI; “A” – 5’ acceptor, “D” – 3’ donor; “E” – enhancer center. B. Tet1 and 5hmC enrichment before and after RA treatment at Tet1’s differential sites defined by diffReps, filtered by active enhancers, including 3 Kb flanking regions. The differential sites are ranked by the “diff” algorithm. The up and down sites are plotted separately. Both average profiles and heatmaps are shown. “L” – genomic left, “R” – genomic right as lower coordinates are to the left of higher coordinates.