Figure 6

Common unfolding of gene expression responses. The short-term responses of steady-state yeast to pulses of nutrient discussed in [28] and the stress responses of [29] show a transient peak of up/down regulation. The peaking times are substantially uniform on the genes. For each gene we compute the maximal signed amplitude at the peak and lump together genes belonging to each of the known protein complexes (see Fig. S5 in Additional file 1). If for [28] we compare this amplitude with the phase (left) and the pulse width (right) of the corresponding genes for the YMC, we can observe that both scatter plots have a consistent anticorrelation: complexes upregulated in the glucose stimulations of [28] correspond roughly to "early" complexes in the YMC and also to genes with a fast turnover. At the other end, complexes downregulated in [28] are late in the YMC and are more stable, see (a). This shows how, in spite of different growth and stimulation conditions, the gene expression program is substantially faithful. On the contrary stressful stimuli such as those described in [29] yield correlated pattern with phase/width of the YMC (b). Just like for the YMC, for both types of responses cytoplasmic translation behaves differently from the mitochondrial one. In red circles the first 3 complexes of Fig. 3(c) are highlighted, in magenta squares their mitochondrial counterparts. Hence the anomaly represented by cluster 9 of Fig. 1 with respect to the HL classification is confirmed by these other dynamical responses.