Figure 3

Effective gene networks and metabolic coherence. (A) Scheme depicting the calculation of the metabolic coherence ratio MCR for afictitious network and data set. The data (genes with significantly changed expression) are mapped onto the network resulting in an effective subnetwork. The metabolic control ratio is then the ratio of connected nodes (blue) and all nodes, i.e. the sum of connected and isolated (red) nodes, in the effective network. Unhighlighted nodes correspond to genes with no significant expression changes. (B) Calculation of the metabolic coherence. Randomly reselecting the same number of affected nodes in the network allows the sampling of random effective networks and thus the computation of a set of random metabolic control ratios MCR'. These allow the computation of a z-score value termed metabolic coherence MC for the MCR. (2) is an example of a real effective network, whereas (1) is one of its random counterparts. MCR' of (1) lies approximately around the mean <MCR' >.