Fig. 1

Expression, H3K4me3, H3K27me3 and RNAPII (8WG16) signatures at promoters of 22,179 genes in eight mouse cell types. a Hierarchical clustering of normalised expression values (see Methods) across eight cell types results in a tree where biological relationships between cell types are largely reconstituted. b Hierarchical clustering of average normalized RNA-seq signal (reads per million -RPM) across the gene promoters (±5 kb) for eight cell types. c Hierarchical clustering of H3K4me3 marked promoters across all cell types results in a tree in agreement with the known developmental relationships between cell types. d The average number of H3K4me3 detected peaks at the promoters is highly consistent across all the cell types. e The average H3K4me3 signal at common peaks across all cell types is highly variant, with BMDMs showing the strongest signal. f Hierarchical clustering of RNAPII (8WG16) binding is closely correlated with the H3K4me3 tree, rather than the expression tree. g The average number of RNAPII peaks at the promoters is consistent across cell types, however less than in H3K4me3 marked promoters. h The average RNAPII signal at common peaks at the promoters is highly variant with ESCs displaying the strongest signal. i Hierarchical clustering of H3K27me3 marked promoters across all cell types results in a tree where only the relationships of MBs and MTs are reconstituted. j The average number of H3K27me3 peaks at the promoters is variable across the cell types, with B cells showing the largest number of detected peaks in all cell types. k The average H3K27me3 signal at common peaks is highly variant across cell types with MEFs showing the strongest signal