Fig. 5

RNAPII pausing across clusters and cell types. a Distribution of pausing indices across gene promoters in all 31 clusters in our study. Clusters are ordered according to their mean pausing index. The colours in the background denote the level of RNAPII pausing - grey: no pausing, yellow: low pausing, red: mid pausing, dark red: high pausing. b Distribution of expression levels (log2(FPKM+ 1)) of genes in each cluster. The clusters arranged in the same order as in Fig. 5a. The colour background denotes a threshold on expression (log2(FPKM+ 1) =1) as defined in Additional file 1: Figure S1 – grey: lowly or not expressed, green: expressed. c Four representative clusters displaying four combinations of RNAPII pausing and gene expression. d Distribution of developmental (GO:0045165, GO:0048864, GO:0007498) and cell cycle (GO:0007049) genes across clusters. e RNAPII pausing vs expression for developmental and cell cycle genes (see Methods) across cell types. f Mean pausing indices for diverse gene sets in each cell type. The gene sets were developmental, cell-cycle as well as bivalent, H3K4me3-only and H3K27me3-only genes in ES cells