On the incongruence of genotype-phenotype and fitness landscapes
Fig 6
Global incongruence: Genotype-phenotype landscapes of transcription factor-DNA interactions.
Landscapes constructed using (A,B) the mismatch model and (C,D) experimental measurements from protein binding microarrays for 1,137 eukaryotic transcription factors. (A) The number of genotypes, shown in relation to mismatch class. (B) The absolute change in the number of peaks in the fitness landscape, relative to the genotype-phenotype landscape, shown in relation to the optimal mismatch class mopt. Labels indicate the number of genotypes per peak in the fitness landscape. Note the symmetry in the absolute change in the number of peaks around mismatch class mopt = 4, as well as the tripling of the number of genotypes per peak for each increment in mopt. The grey shaded circles are a schematic representation of the growing width of the peaks. (C) The number of genotypes per binding affinity class, where protein binding microarray E-scores are used as a proxy for relative binding affinity. Violin plots show the distribution, and box-and-whisker plots the 25–75% quartiles, across genotype-phenotype landscapes for the 1,137 transcription factors. Closed symbols and the dashed line denote the median of each distribution. (D) Violin plots of the distribution of the absolute change in the number of peaks in the fitness landscape, relative to the genotype-phenotype landscape, shown in relation to the optimal binding affinity wopt for σ = 0.15. The inset shows the mean absolute change in the number of peaks, in relation to wopt. The x-axes in (A,B) are arranged such that binding affinity increases when read from left to right, in qualitative agreement with the x-axes in (C,D). The results in panels A-C are independent of σ.