For each experiment, using significantly perturbed processes as determined by GSEA and the subnetwork induced by the set of perturbed interactions D as the inputs, we computed BPLNs as described by Dotan-Cohen et al.[ 13].
The vector of normalized steady states measured in the k-th perturbation experiment (where node k is perturbed) is denoted by x k, i.e. x i k is the state of the i-th node in experiment k.
Together, these experiments corroborate that a perturbed Bcd gradient during cycles 11 13 can lead to normal patterning during cycle 14 to gastrulation.
In two independent experiments, 24 proteins with perturbed expression patterns were identified (P < 0.05, ANOVA) (Fig. 6); 15 proteins had decreased expression and 9 were increased.
These predictions were required for an experiment where the network is perturbed simultaneously with a 10-fold decrease of r9 kd, a 2-fold increase in rbs3 strength and a 10-fold increase of rbs5 strength.
These classical knockout studies are however based on single-perturbations: In each experiment, a single element in the system is perturbed, and the resulting phenotype is used to identify its function.
Detailed analysis of the atmosphere-ocean interaction as well as perturbed physics ensemble experiments including the ocean component might be useful for identifying the physical mechanisms (Collins et al. 2006).
This information gain can be used to choose those genes that will be perturbed in subsequent experiments in order to refine our knowledge about the architecture of an underlying gene regulatory network.
To illustrate the robustness and quality of solutions obtained, computational experiments are performed based on 1000 perturbed demand matrices.
