Fig. 5: Quantitative association between subgenome-biased TF binding and expression.
From: Transposable elements orchestrate subgenome-convergent and -divergent transcription in common wheat
a Illustration of the quantitative divergence of TF binding in the promoters of triad genes. The relative binding of AP2-ERF-6D-1 is presented. Orange dots represent the balanced regulatory pattern. Blue and gray dots represent the unbalanced regulatory pattern. b Fraction of balanced and unbalanced TF binding in the promoters of triad genes (1:1:1 correspondence across subgenomes). c Bar plot presenting the results of the quantitative analysis of the balanced and unbalanced binding of AP2-ERF-6D-1 and NAC-6A-1. d Correlation of subgenome-biased binding and expression. Homoeologous gene pairs were grouped according to the regulatory divergence, which was calculated as the sum of the binding of all TFs |log2(fold-change)| in the promoter regions. The expression divergence was calculated as the |log2(fold-change)| of two orthologous genes. The two-tailed Wilcoxon signed-rank test was used to compare expression divergence between subgenomes A and B (n = 8412), B and D (n = 6658), A and D (n = 8561), respectively. Horizontal lines in boxplots show median, hinges show IQR, whiskers show 1.5 × IQR, points beyond 1.5 × IQR past hinge are shown. Source data are provided as a Source Data file.
