Figure 4.

The measured occupancy profiles of individual GTFs are significantly affected by nonconsensus TF-DNA binding. The average free energy of nonconsensus TF-DNA binding per basepair, $\langle f\rangle ={\langle {\langle F\rangle }_{\text{TF}}\rangle }_{seq}/M$, and the average occupancy profile of individual GTFs from Rhee and Pugh (4) around the TSSs of 3945 genes. To compute error bars, we divided genes into five randomly chosen subgroups and computed $\langle f\rangle$ for each subgroup. The error bars are defined as one standard deviation of $\langle f\rangle$ between the subgroups. The error bars for the GTF occupancy are computed analogously. We used $M=8$ in all calculations. The linear correlation coefficient is computed in each case for a linear fit of $\langle f\rangle$ versus the average GTF occupancy at individual genomic locations, every 20 bp, within the interval $(-990,990)$.