Figure 6.

RTR of a Myc-E2F pair. We calculated the observed RTRs of Myc-E2F from simulations with and without an additional space constraint between two TFBSs, and compared the observed and expected RTRs assuming independence. The fit-1 lines are expected values based on the mean turnover rate of individual TFBSs, and the fit-2 lines are expected values based on median turnover rate of individual TFBSs. Under simulation without space constraints between the sites, the expected RTRs are close to the observed ones in both cases: (a) replacement turnover occurred at both Myc and E2F sites; (b) replacement turnover occurred at only one of two sites. Under simulation with space constraint, the expected RTRs are higher than the observed ones when (c) replacement turnover occurred at both Myc and E2F sites, but are close to observed ones when (d) replacement turnover occurred at only one of the two sites. The models based on estimates of turnover for individual sites given in equations 3 and 4 fit the observed RTR data well in those cases where no dependency between sites exists.

Huang et al. Genome Biology 2007 8:R225   doi:10.1186/gb-2007-8-10-r225
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