Figure 4
From: Genome-wide analysis of transcription factor binding sites and their characteristic DNA structures
Structural levels of DNA sequences are significantly correlated with TF-DNA binding affinities. (A) Shown is a scatter plot comparison between structural (duplex disrupt energy) levels of 8-mers and TF Dal80 binding affinities of 8-mers. To control for nonspecific protein-DNA binding, we restricted the analysis to the top 500 out of 65,536 8-mers with the highest Dal80 binding affinities. The Pearson correlation and the p-value of the scatter plot are indicated. The duplex disrupt energy property of DNA sequences facilitates Dal80 binding to DNA. (B) Same as (A), but for TF Swi4 and structure roll. To control for nonspecific protein-DNA binding, we restricted the analysis to the top 500 out of 65,536 8-mers with the highest Swi4 binding affinities. The roll property of DNA sequences inhibits Swi4 binding to DNA.