Figure 4

The dependency matrix for the yeast glucose repression network. Each element in the matrix shows the relationship between an effecting species and an affected species, specified at the bottom of the column and at the end of the row, respectively. A yellow field in the intersection of the i^th column and j^th row signifies that the i^th species is an ambivalent factor with respect to the j^th species, i.e. that both activating and repressing/inhibiting paths from the i^th to the j^th species exist. For example, the yellow color of the first element (first column and first row) indicates that both inhibiting and activating paths exists from exterior glucose to the Sip4 protein, i.e., exterior glucose is an ambivalent factor with respect to Sip4. Similarly, a dark green field and a light green field indicate a total and a non-total activator, respectively, i.e., only activating paths exist and negative feedback loops are either absent (total) or present (non-total). Dark red and light red fields represent total and non-total repressors/inhibitors, respectively. A black field indicates that no path exists from A to B. The large number of black columns in the middle corresponds to output species (sinks), which per definition are non-affecting towards all species. Due to the directional nature of the interaction network, the matrix is not symmetric (e.g. Sip4 is non-affecting toward exterior glucose). See nomenclature note for gene and protein species in the legend of Figure 3.