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Fig. 2 | BMC Bioinformatics

Fig. 2

From: Boolean regulatory network reconstruction using literature based knowledge with a genetic algorithm optimization method

Fig. 2

In silico experiments and attractor reachability graph. Example of attractor reachability graph for the transition from unperturbed network to over-expression of TNF on the cell-fate decision model [11]. The unperturbed network has four attractors, each shown as a network with red nodes corresponding to active nodes and blue nodes corresponding to inactive nodes. These attractors are labelled A1,1, A1,2, A1,3, and A1,4. Attractor A1,3 corresponds to the physiological state used by Calzone and co-authors [11] as initial state. The perturbed network (TNF fixed to 1) has only three attractors (denoted A2,1, A2,2 and A2,3), interpreted as the three cell fates: non-apoptotic cell death, survival, and apoptosis. After TNF over-expression, each attractor of the unperturbed network will stabilize into at least one attractor of the perturbed network (grey arrows). For example, the physiological state A1,3 will stabilize into either of the three cell fates A2,1, A2,2 and A2,3. Note that this figure presents only the transition from unperturbed network to over-expression of TNF, and not the reverse transition. Therefore no information is shown on the reachability from attractors obtained with over-expression of TNF to attractors of the unperturbed network

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