Evolution of Stress-Regulated Gene Expression in Duplicate Genes of Arabidopsis thaliana
Figure 6
Correlation between stress response and cis-regulatory evolution.
(A) Enrichment of putative cis-elements in the putative promoter regions of stress responsive genes under different conditions (includes different time points for each treatment, e.g., drought 3 hr, drought 6 hr, etc.). Significant enrichment of a particular cis-element in the promoters of up-regulated, down-regulated, or both up- and down-regulated genes is indicated by blue, yellow, and red, respectively. No significant enrichment under a condition is indicated by a white box. (B) Contour plot illustrating the positive correlation between stress response and putative cis-element asymmetries. Cis-element Asy is defined in the same way as for stress response partitioning (Figure 5A) except that, presence (1) or absence (0) of a putative cis-element was used in place of up-regulation (1) and no change (0). For a particular duplicate pair, we randomly assigned index 1 and 2 to the duplicates, so that when we calculated asymmetry score (Asy, Figure 5A) for partitioning of responsiveness and cis-elements, the subtractions were in the same direction. As a result, half of the time Asy is below zero. The observed number in each Asy value bin was compared to simulated datasets generated by random assignment of putative cis-elements among extant genes while fixing the number of genes with a particular element. The deviation of the observed numbers from random expectation was assessed by calculating the Z-score. Shades of red and blue indicate over and under-representation, respectively.