Evolution and Selection in Yeast Promoters: Analyzing the Combined Effect of Diverse Transcription Factor Binding Sites
Figure 4
Shown are inferred selection factors, compared for pairs of similar target k-mer sets on alignment of S. cerevisiae promoters with different yeast species. C, the correlation between the σ values in the two models. R, the root mean square difference value. The high correlation among the inferred σ values indicates that our model successfully decomposes the background mutation rate (which is different for each species) and the selection on each TFBS (which is quite stable as seen here).
(A,D,E) Comparison of σ values in the literature-based model for each pair of species.
(B) The literature-based model using ChIP-bound promoters only on cerevisiae-paradoxus alignments compared to the same model on cerevisiae-mikatae alignments.
(C) The de novo model on cerevisiae-paradoxus alignments compared to the same model on cerevisiae-mikatae alignments.