Expression Matrix

In order to infer a boolean genetic network, a population of cells containing a target genetic network is monitored in the steady state over a series of M experimental perturbations. In each perturbation P_m ( $0 \leq m < M$) any number of nodes may be forced either to a low or a high level. Genes may be perturbed through laboratory methods for gene deletion or overexpression, while stimuli are perturbed by altering the environment outside the cell. The observed steady-state expression levels for all genes and stimuli over all experimental perturbations or over time are represented by the expression matrix E. Figure 14.8 shows an expression matrix generated by several illustrative perturbations. Rows of E represent perturbation conditions while columns represent node values in each steady-state condition, such that matrix entry E_ij is the expression level of node X_i in the presence of perturbation P_j. The symbols "+" and "-" are used to show that a node has been forced to a high or low value, respectively.

  

Figure: Expression Matrix - adapted from [5]