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Table 1 PRISM commands modeled signaling pathway

From: FoPA: identifying perturbed signaling pathways in clinical conditions using formal methods

No.   PRISM Language Specification
(1) A → B Activation [ ]A > 2 & (B = 1 |  B = 2) → probactive : (B = (A = 3 & B = 1) ? 3 : 4) + (1 − probactive) : (B = 0);
(2) A B Inhibition [ ]A < 3 & (B = 1 | B = 2) → probinhibit1 : (B = B + 2) + (1 − probinhibit1) : (B = 0);
[ ]A > 2 & (B > 2) → probinhibit2 : (B = B − 2) + (1 − probinhibit2) : B = 0;
(3) A \( \overset{+p}{\to } \) B Phosphorylation activation [ ]A > 2 & (B = 1 | B = 2) → probactive : (B = (A = 3 & B = 1) ? 3 : 4) + (1 − probactive) : (B = 0);
(4) A +p B Phosphorylation inhibition [ ]A < 3 & (B = 1 | B = 2) → probinhibit1 : (B = B + 2) + (1 − probinhibit1) : (B = 0);
[ ]A > 2 & (B > 2) → probinhibit2 : (B = B − 2) + (1 − probinhibit2) : B = 0;
(5) A \( \overset{-p}{\to } \) B Dephosphorylation activation [ ]A > 2 & (B = 1 |  B = 2) → probactive : (B = (A = 3 & B = 1) ? 3 : 4) + (1 − probactive) : (B = 0);
(6) A p B Dephosphorylation inhibition [ ]A < 3 & (B = 1 | B = 2) → probinhibit1 : (B = B + 2) + (1 − probinhibit1) : (B = 0);
[ ]A > 2 & (B > 2) → probinhibit2 : (B = B − 2) + (1 − probinhibit2) : B = 0;
(7) A → B Indirect effect [ ]A > 2 & (B = 1 | B = 2) → probactive : (B = (A = 3 & B = 1) ? 3 : 4) + (1 − probactive) : (B = 0);
(8)   A is not activated nor inhibited by other genes [ ] (A = 1 | A = 2) → probinit : (A = A + 2) + (1 − probinit) : (A = 0);
(9) initializing the variables Aexpressed genes [ ] (A =  − 1) → prob1 : (A = 1) + prob2 : (A = 2)
A  differentially expressed genes [ ] (A =  − 1) → prob1 : (A = 1) + prob2 : (A = 2)
  1. Activation, Phosphorylation activation, Dephosphorylation activation, and Indirect effect are all different types of activation in which gene A activates the gene B. Thus, they model the same as the Activation relation. Likewise, the Inhibition, Phosphorylation inhibition, and Dephosphorylation inhibition are all different types of inhibition in which gene A prevents the activation of gene B and they model the same as the Inhibition relations. The probs are the parameters for the commands that are replaced with the appropriate values when the model is constructed. A and B in PRISM command are variables indicating the states of the genes A and B respectively