Table 2.

Biological interpretation based on literature and assignment of each process in Figure 6

Wet experiments results published in literature	#1	#2	Reaction type	Refs
Translocation of LIN-3 emanated from AC to P5.p and P7.p	p1	LSMass(m1*0.1*low, 0.1)	Translocation	[9,35]
Translocation of LIN-3 emanated from AC to P3.p, P4.p and P8.p	p2	LSMass(m1*0.1*mid, 0.1)	Translocation	[9,35]
ligands LIN-3 binding to LET-23 to form a ligand-receptor complex	p3	LSMass(m1*0.1*high, 0.1)	Binding	[43,44]
Two identical LIN-3 LET-23 complex combining to form a dimer	p4	LSMass(m3*0.1, 0.5)	Dimerization	[43,44]
Autophosphorylation following the dimerization of ligand-receptor complex	p5	LSMass(m4*0.1, 0.5)	Autophosphorylation	[43,44]
SEM-5 is activated by LIN-3 LET-23 dimer	p6	LSMass(m5*m6*0.1, 0.5)	Enzymic reaction	[9,35]
LET-60 is activated by upstream SEM-5	p7	LSMass(m7*m8*0.1, 0.5)	Enzymic reaction	[9,35]
Inactive MPK-1 is activated by upstream LET-60	p8	LSMass(m9*m10*0.1, 0.5)	Enzymic reaction	[9,35]
The movement of MPK-1 from cytoplasm to nucleus	p9	LSMass(m11*0.1, 0.5)	Translocation	-
Active MPK-1(N) downregulates the target genes of lst and transcribes the mRNA of lateral signal (LS)	p10	LSMass(m12*0.1, 0.5)	Transcription	[9]
LS mRNA is translated to LS molecules	p11	LSMass(m17*0.1, 0.5)	Translation	-
Translated LS molecules are released to combine with	p12	LSMass(m19*0.1, 0.5)	Translocation	[34]
LIN-12 receptors
LIN-31/LIN-1 complex is dissociated to individual active	p13	LSMass(m12*m13*0.1, 0.5)	Phosphorylation	[38,45]
LIN-31 and LIN-1 by the phosphorylation of active MPK-1
Active a MPK-1(N) acts as transcription factor to tran-	p14	LSMass(m14*0.1, 0.5)	Transcription	[42]
scribe vulval genes to mRNA
mRNA of vulval genes is translated and cause the 1	p15	LSMass(m16*0.1, 0.5)	Translation	[42]
cell fate
LIN-12 receptor received the LS molecules from the ad-	p16	LSMass(m20*mκ*1.0, 0.1)	Binding	[32,34]
jacent Pn.p and shape a ligand-receptor complex
LIN-12 receptor received the LS molecules from its own	p17	LSMass(m20*mκ*1.0, 0.1)	Binding	[32,34]
Pn.p and shape a ligand-receptor complex
LIN-12 receptor received the LS molecules from the ad-	p18	LSMass(m20*mκ*0.1, 0.1)	Binding	[32,34]
jacent Pn.p and shape a ligand-receptor complex
Binding of LS ligands to LIN-12/Notch receptor leads to	p19	LSMass(m21*0.1, 0.5)	Shedding/Cleavage	[34]
shedding of the LIN-12/Notch extracellular domain via cleavage
Cleaved intracellular domain of LIN-12/Notch receptor move from cytoplasm to nucleus	p20	LSMass(m23*0.1, 0.5)	Translocation	[34,46]
Cleaved LIN-12/Notch receptor promote the target lst genes transcribed into mRNA of lst genes	p21	LSMass(m24*0.1, 0.5)	Transcription	[34,36]
LST mRNA is translated to LST in cytoplasm	p22	LSMass(m26*0.1, 0.5)	Translation	-
LIN-12 immediately induces lst expression thus prevents cells from engaging the mechanisms reducing LIN-12 activity	p23	LSMass(m20*lin12_init, 0.1)	Production	[9]
LIN-3 emanating from hyp7 binds to LET-23 to form a complex	p24	LSMass(m2*m28*0.1, 0.5)	Expression	[9,37]

Table 2: The column of #1 represents corresponding processes in the HFPNe model. Twenty-four events are assigned to the processes p_i ∈ {p₁, ⋯, p₂₄}. Each reaction speed of the processes is assigned as shown in the column of #2, in which several reaction speeds have been tuned manually. Reaction types of the processes are described in the fourth column with the literature facts given in the fifth column. Variable m_x ∈ {m₁, ⋯, m₃₂} denotes the concentration of corresponding substance (see Table 3). The variable mk is used to collectively denote the concentration of the LS molecules generated from the adjacent Pn.p. The values of high, mid, and low are assigned to 100, 1, and 0.01. For example, the process p₉ has a reaction speed with a noise denoted by LSMass(m₁₁ *0.1, 0.5), i.e., the reaction speed depends on the concentration of MPK-1{active} (C) in the cytoplasm (m₁₁). LSMass() is a function of log-normal distribution (see text).