Figure 2.

Statistical model of RPol II distribution of Bi-peak shape. (A) RPol II binding fragments on 2 promoters form a bi-peak shape. Green and blue dotted lines represent the RPol II distribution surrounding TSSs of 2 opposite genes. The red line presents the accumulation of RPol II fragments. P1, P2, and V are 3 features of the bi-peak shape. The parameters, Sig and Dif, are used to identify the bi-peak shape of RPol II distribution in bidirectional regions.(B) A statistical model of RPol II binding pattern surrounding theTSSs of bi-directional gene pairs. The adjacent genomic regions are divided into multiple 20-bp bins, in which the number of RPol II fragments is assumed to follow a Poisson distribution for each promoter. For each of these, the overall binding pattern coud be characterized by 5 hidden variables, including 3 variables describing the expected number of fragments in the background region (B), the transcript region (T), and the bin that contains TSS (S), and 2 variables modeling the signal decay rates in both upstream and downstream of the TSS (Kp and Kt). Each hidden variable follows a gamma distribution genome-wide. For the accumulation of RPol II fragments of two promoters, the number of RPol II fragments also follow a Poisson distribution.

Wang et al. BMC Medical Genomics 2013 6(Suppl 1):S5   doi:10.1186/1755-8794-6-S1-S5