Table 1 PRISM commands modeled signaling pathway

(1)

A → B

Activation

[ ]A > 2 & (B = 1 |  B = 2) → prob_active : (B^′ = (A = 3 & B = 1) ? 3 : 4) + (1 − prob_active) : (B^′ = 0);

(2)

A ⊣ B

Inhibition

[ ]A < 3 & (B = 1 | B = 2) → prob_inhibit1 : (B^′ = B + 2) + (1 − prob_inhibit1) : (B^′ = 0);

[ ]A > 2 & (B > 2) → prob_inhibit2 : (B^′ = B − 2) + (1 − prob_inhibit2) : B^′ = 0;

(3)

A \( \overset{+p}{\to } \) B

Phosphorylation activation

[ ]A > 2 & (B = 1 | B = 2) → prob_active : (B^′ = (A = 3 & B = 1) ? 3 : 4) + (1 − prob_active) : (B^′ = 0);

(4)

A ⊣^+p B

Phosphorylation inhibition

[ ]A < 3 & (B = 1 | B = 2) → prob_inhibit1 : (B^′ = B + 2) + (1 − prob_inhibit1) : (B^′ = 0);

[ ]A > 2 & (B > 2) → prob_inhibit2 : (B^′ = B − 2) + (1 − prob_inhibit2) : B^′ = 0;

(5)

A \( \overset{-p}{\to } \) B

Dephosphorylation activation

[ ]A > 2 & (B = 1 |  B = 2) → prob_active : (B^′ = (A = 3 & B = 1) ? 3 : 4) + (1 − prob_active) : (B^′ = 0);

(6)

A ⊣^−p B

Dephosphorylation inhibition

[ ]A < 3 & (B = 1 | B = 2) → prob_inhibit1 : (B^′ = B + 2) + (1 − prob_inhibit1) : (B^′ = 0);

[ ]A > 2 & (B > 2) → prob_inhibit2 : (B^′ = B − 2) + (1 − prob_inhibit2) : B^′ = 0;

(7)

A → B

Indirect effect

[ ]A > 2 & (B = 1 | B = 2) → prob_active : (B^′ = (A = 3 & B = 1) ? 3 : 4) + (1 − prob_active) : (B^′ = 0);

(8)

A is not activated nor inhibited by other genes

[ ] (A = 1 | A = 2) → prob_init : (A = A^′ + 2) + (1 − prob_init) : (A^′ = 0);

(9)

initializing the variables

A ∈ expressed genes

[ ] (A =  − 1) → prob₁ : (A^′ = 1) + prob₂ : (A^′ = 2)

A ∈ differentially expressed genes

[ ] (A =  − 1) → prob₁ : (A^′ = 1) + prob₂ : (A^′ = 2)