Figure 4. Arboretum reconstruction of expression module evolution (Analysis 1).
(A) Five expression modules identified by Arboretum in the transcriptional response to glucose depletion. Each row corresponds to a species (tree, left) and each major column to a module (1–5, labels top). Module labels are color coded by the regulation of the module’s genes following depletion, as noted on top, from bright blue (Module 1) for strong repression to bright red (Module 5) for strong induction. Each module’s height is proportional to the number of genes in the module. The five columns in each module are the expression levels at lag (L), late log (LL), diauxic shift (DS), post-shift (PS), and plateau (P) relative to mid-log phase. Red: induced; blue: repressed; white: no change. (B)–(F) Module assignments in all extant and ancestral species (see Figure 5B for ancestral node assignment). Each matrix corresponds to the genes in one of the five modules in the LCA (A14) (B: Module 1; C: Module 2; D: Module 3; E: Module 4; F: Module 5), and shows the module assignment of these genes in each of the extant and ancestral species from S. cerevisiae (leftmost column) to the LCA (rightmost column). The biological functions listed at the top of each module are representative labels chosen based on Gene Ontology terms enriched in all species in that module (Supplementary file 1). The range of FDR p values and fraction of genes in each module are as follows: Module 1: Ribosome biogenesis, p<5.28 × 10−48 to 1.25 − 10−119, fraction 37.3–61.6%. Module 2: cell division, p-value<3.51 × 10−02 to 4.52 × 10−02, fraction 9–33.6%. Module 3: cell morphogenesis, p<4.64 × 10−02 to 4.95 × 10−02, fraction 6.5–81%. Module 4: mitochondrial, p<3.20 × 10−02 to 4.90 × 10−02, fraction 2.4–37.9%; proteasome, p<3.85 × 10−04 to 3.97 × 10−02, fraction 1.6–15%. Module 5: respiration p<4.77 × 10−02 to 4.8 × 10−02, fraction 32.6–58.9%; response to stress, p<4.75 × 10−02 to 4.86 × 10−02, fraction 2.6–13.7%. Module assignment in each species is marked by a color code, as in the top of panel A (bright blue: Module 1; light blue: Module 2; white: Module 3; pink: Module 4; red: Module 5). Species are ordered by post-fix ordering (left-child, right-child and parent) of the species tree, as marked on the legend (bottom). Black bars indicate points of phylogenetically coherent divergence in expression of orthologous genes, as discussed in the text.
DOI: http://dx.doi.org/10.7554/eLife.00603.011