Figure 4

Profiles of transcription and chromatin-related patterns as a function of gene expression. (a-d) Probe signals for Pol II (a), histone H3 (b), H3K36me3 (c), and FAIRE (d) were used to generate average spliced gene profiles that were grouped into ten ranked bins based on Affymetrix expression data. Average values for each bin within each expression group were plotted on the same absolute scale for each experiment type. For panel (a), the background level of RNA Pol II enrichment was estimated by calculating the average signal from all probes (152,253) that fell outside of binned regions for analysis. This background average is shown as a horizontal blue solid line. Because some atypically large untranslated regions and novel annotated regions will also contribute signal to this value, a second average (horizontal blue dotted line) is shown where the top 10% of probes by signal (15,226) are removed. The red-to-green color bar at the bottom of the figure depicts average expression levels of bins (red, high expression; green, low expression), and black vertical lines within each box demarcate different sections within the average gene.