Fig. 1

Simplified representation of the GRN model in CABERNET. a Example RBN with 3 genes (nodes) and edges representing regulatory interactions (via node-specific Boolean functions, not shown). b Example dynamics to highlight network’s attractors, modeling gene activation patterns A ₁, …, A ₄, and possible transitions among them induced by noise (i.e., single flips). c The transitions yield an Attractor Transition Network that generates 5 cellular types when 3 thresholds, δ _i , i=1,2,3 are evaluated to asses the corresponding Threshold Ergodic Sets. In this approach, where the efficiency of noise-control mechanisms is related to differentiation types, stem cells (pink), intermediate stages (light blue) and fully differentiated cells (yellow, purple and grey) emerge. The corresponding differentiation tree, is shown (Fig. modified from [35])