Figure 1.

An example of FAIRE, Pol II ChIP-chip, and expression data. The top and bottom panels with green points depict expression data for the upper and lower strand, respectively, obtained from random-primed RNA hybridized to Affymetrix tiling arrays with each point representing a single probe. The second and fourth panels show annotated genes in the region around sec21 (SPAC57A7.10c), with exons numbered underneath the gene. The third panel shows a 5 probe running average of Pol II signals (black points) or FAIRE signals (pink/red points). The horizontal red line shows the 85% percentile line for all FAIRE probe signals, with probes above this cut-off colored red and those below colored pink. Note that FAIRE and Pol II signals are not strand-specific.