Dissecting Dynamic Genetic Variation That Controls Temporal Gene Response in Yeast
Figure 5
Co-associated genes typically share a similar pattern of genetic effects over time.
(A) Six gene modules (column 1), constructed on the basis of a shared trans-associated genetic variant (a genomic interval; column 2), are listed together with their known causal gene, if available (column 3; †-cis-associated causal gene, references are in parentheses) and the number of associated genes in a module (column 4). Significant enrichments in biological processes are detailed in column 5. Significant enrichments of temporal two-state patterns in each module are presented together with the description of these enriched patterns (columns 6 and 7, respectively). (B−E) Gene expression and genetic effects in modules nos. 1 (left), 3 (middle) and 4 (right). Gene expression (B) and genetic effect (C) of representative genes, as well as genetic effects of an entire module (D); plots are shown as in Fig. 4B. (E) Average gene expression (y-axis) at six time points (x-axis) for the known causal gene of each module. For cis-associated causal genes (modules nos. 3 and 4), brown and black indicate strains carrying the RM and BY alleles, respectively. The plots demonstrate the good match between the timing of abrupt changes in causal genes (E) and the timing of alterations in the observed genetic effects of their associated target genes (D).