Figure 1. Determination of Pol-II active-region/gene associations and changes to gene activation state for specific genes. RNA-Polymerase-II (Pol-II) ChIP-on-chip data could be examined on any continuous scale from entire chromosomes to single genes. Determination of Pol-II active regions, the association of active regions to genes, and the calculation of specific metrics for each region, required the sequential use of TAS and the TransPath program. A: First, TAS generated interval tracks where Pol-II signal levels were above an intermediate threshold. This is illustrated for a region surrounding Pde6B, a key marker of photoreceptor terminal maturation. Second, interval track data were processed using TransPath to determine active regions. Active regions were comprised of one or more interval tracks in close proximity. Two active regions are illustrated in the P25 neural retina. B: Higher resolution view of the active region surrounding the Pde6b TSS. Signals for individual tiling probes (35 bp spacing) are visible. For each active region, TransPath calculated specific metrics, such as the Pol-II peak signal ratio (P25/P2), as illustrated by the vertical black bars indicating signal maxima from the P25 and P2 time point samples. Genes in view: Phosophodiesterase 6b (Pde6b), Polycomb group ring-finger 3 (Pcgf3), Complexin 1 (Cplx1).