Figure 4

Distribution of RNAPII along the gene length and enriched pathways. (A) The plots represent the average distribution along the gene of probes (with p <0.05) associated with each form of RNAPII. The start codon is taken as “0”. Data are organized into bins ranging from -500 bp upstream of the ATG to +4000 bp downstream and plotted against the percentage of total probes falling into each bin. The position of a probe along the x axis is the average of the positions of all probes within a given bin. While all genes are aligned at the ATG (“0”), they terminate at a wide range of positions downstream with an average at +2.5 kb. The plots on the right show the distribution of early/positive and late/positive loci (r >0.4), while those on the left plot the distribution of early/negative and late/negative loci (r <0.4). (B-C) The plots represent the average distribution of the genetic loci associated with each form of RNAPII as a function of gene length. Position distributions were plotted as histograms for each gene group with intervals of 500 bp from -2 kb to +5 kb. Histograms were plotted to display the binding positions in 500 bp intervals from -2 kb to 5 kb flanking the translational start codon at 0. A goodness-of-fit test was performed within each bin to calculate the probability of that region being equally bound by RNAPII for different gene groups. Regions with binding bias by group were assigned p <0.05 using the chi-square test. Data were assessed in this manner for (B) early/positive and late/positive and (C) early/negative and late/negative subsets. (D) Functionally enriched pathways (p <0.05) for each of the four gene groups. Colors refer to the three distinct databases that were used for pathway enrichment analysis.