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. 2015 Mar 10;108(5):1257–1267. doi: 10.1016/j.bpj.2014.12.037

Figure 5.

Figure 5

Accessibility of individual sites is utilized by GEMSTAT-A to improve predictions. Details of GEMSTAT-A modeling on enhancers gt_(−1), pdm2_(+1), and cnc_(+5) are shown in the left, middle, and right columns, respectively. (A) Change in goodness of fit (ΔwPGP) of GEMSTAT-A predictions when a binding site’s accessibility score is forced to a value of 1 (maximum accessibility), shown for each site as a function of its location in the enhancer. (B) Reduction in estimated binding energy (ΔΔE) due to local accessibility is shown for each annotated binding site as a function of the site’s location in the enhancer sequence. Only sites for a subset of TFs (repressors at left and activators at middle and right) are shown. (C) Predicted expression profiles of GEMSTAT-A (orange lines) compared to GEMSTAT predictions (purple lines) and experimentally determined readouts (black lines).