The modular architecture of genome-wide timing control. (a, left) Network of significant heterochronic interactions between 1828 module-specific genes, grouped by module. Interactions are defined by strongly correlated changes in expression timing (P < 10-4). (Figure S25 in Additional file 1 shows this graph with greater resolution.) (a, right) Heterochronic interaction network from module 3 (black lines); only a subset of genes within 2 degrees of gene Swi5 and that share TFs is shown (dashed blue arrows). Blue nodes indicate significant association of a TF with a module. (b) Novel interaction between Swi5 and Mfa2, which co-cluster in 23/45 comparisons (P = 6.8 × 10-6); four are shown. Timing maps (columns 1, 3) illustrate timing pattern changes between strains for each gene, given parameters (α, β, γ) and Beta CDF: t' = (Beta (α, β) + γ) mod 1. Gray dashed lines indicate no change. Trajectory plots for each gene (columns 2, 4) show the time transformation of CDC-expression from one strain (dashed red line) to another (orange line). Blue lines show a gene's CDC-expression in the respective target strain. Transformation order is reversible, since timepoint maps are invertible. R2 and RMSE fit statistics are shown. * indicates significance (P < 0.05).
Simola et al. Genome Biology 2010 11:R105 doi:10.1186/gb-2010-11-10-r105