Comparison of RNA-seq and ChIP-seq data using S2cells. (a) Scatter plot for H3K4me3 and H3K27me3 enrichment of all annotated genes. A common 0 to +500-bp window with respect to the TSS was used to calculate both H3K4me3 and H3K27me3 reads. The blue dashed lines indicate the statistical cutoff line - P < 0.05 in a 1-kb window per 1 million total reads. Gene numbers in each quadrant are labeled in black. (b) Scatter plot for RNA Pol II enrichment and RPKM values for all annotated genes. All labels are the same as in Figure 2d, except that RPKM = 1 is used as a cutoff for expressed genes. (c) The RPKM value for genes that have two absent calls (2A) in the microarray. (d) Analysis of the RPKM value of transcripts demonstrates that genes with stalled Pol II are weakly transcribed genes. Genes that show an active Pol II profile are expressed at significantly higher levels. Genes with no Pol II profile are expressed at significantly lower levels. The box represents the 25th and 75th percentiles, with the 50th percentile as a black bar. The whiskers refer to outliers that are at least 1.5× the interquartile range from the box. The y-axis represents the RPKM value.