Table 1. Biological relevance and values of the model parameters.

Parameter	Value	Biological interpretation	Reference
a1	1	Oct4 transcription rate
a2	0.0001	basal transcription level of the Oct4 gene	10
a3	1	maximal activation constant of Oct4 transcription at a saturating level of the external signal A	10
A	0	signal A+ concentration	10
a4	0.01	maximal activation constant of Oct4 transcription at a saturating level of the Oct4-Sox2 complex	10
a5	1	effective dissociation constant between Oct4-Sox2 complex and the promoter of Oct4 gene
a6	2	Hill coefficient for Oct4 transcription regulation by Oct4-Sox2 heterodimer
a7	0.0011	activation constant of Oct4 transcription at a basal level of the external signal A	10
a8	0.001	activation constant of Oct4 transcription at a basal level of the Oct4-Sox2 complex	10
a9	0.1	decay rate for the Oct4 mRNA
a10	1	Sox2 transcription rate
a11	0.0001	basal transcription level of the Sox2 gene	10
a12	1	maximal activation constant of Sox2 transcription at a saturating level of the external signal A	10
a13	0.01	maximal activation constant of Sox2 transcription at a saturating level of the Oct4-Sox2 complex	10
a14	1	effective dissociation constant between the Oct4-Sox2 complex and the promoter of Sox2 gene
a15	2	Hill coefficient for Sox2 transcription regulation by the Oct4-Sox2 heterodimer
a16	0.0011	activation constant of Sox2 transcription at a basal level of the external signal A	10
a17	0.001	activation constant of Sox2 transcription at a basal level of the Oct4-Sox2 complex	10
a18	0.1	decay rate for the Sox2 mRNA	27;46–47
a19	0.05	Oct4-Sox2 complex association rate	10
a20	0.5	decay rate for the Oct4-Sox2 heterodimer
a21	0.001	Oct4-Sox2 complex dissociation rate
a22	0.0093	transport rate of the Oct4 protein from cytoplasm to nucleus
a23	0.0081	decay rate for the Oct4 protein in the nucleus	27;46–47
a24	0.5	translation rate of the Oct4 protein
a25	0.00001	decay rate for the Oct4 protein in the cytoplasm	27;46–47
a26	0.0093	transport rate of the Sox2 protein from cytoplasm to nucleus
a27	0.0081	decay rate for the Sox2 protein in the nucleus	27;46–47
a28	0.5	translation rate of the Sox2 protein
a29	0.00001	decay rate for the Sox2 protein in the cytoplasm	27;46–47
b1	1	Nanog transcription rate
b2	1	basal transcription level of the Nanog gene
b3	0.005	maximal activation constant of Nanog transcription at a saturating level of the Oct4-Sox2 complex	10
b4	1	effective dissociation constant between the Oct4-Sox2 complex and the promoter of Nanog gene
b5	2	Hill coefficient for Nanog transcription regulation by the Oct4-Sox2 heterodimer
b6	0.001	activation constant of Nanog transcription at a basal level of the Oct4-Sox2 complex	10
b7	1	inhibition constant of Nanog transcription at a basal level of the Nanog protein
b8	0.000995	constant of a cooperative effect upon an joint impact of Oct4-Sox2 and Nanog proteins on Nanog transcription	10
b9	1	effective dissociation constant between the Nanog protein and the promoter of the Nanog gene
h	2	Hill coefficient for Nanog transcription regulation via Nanog autoinhibition mechanism
b10	0.005	decay rate for the Nanog mRNA	27;46–47
b11	0.0093	transport rate of the Nanog protein from cytoplasm to nucleus
b12	0.0081	decay rate for the Nanog protein in the nucleus	27;46–47
b13	0.5	translation rate of the Nanog protein
b14	0.00001	decay rate for the Nanog protein in the cytoplasm	27;46–47
c1*	0.0001	basal transcription level of pluripotency factors
c2	0.1	maximal activation constant for transcription of pluripotency factors at a saturating level of the Oct4-Sox2 complex
c3	0.1	constant of a maximal cooperative effect upon an joint impact of Oct4-Sox2 and Nanog proteins on transcription of pluripotency factors
c4	0.001	activation constant for transcription of pluripotency factors at a basal level of the Oct4-Sox2 complex
c5	0.01	constant of a cooperative effect upon an joint impact of Oct4-Sox2 and Nanog proteins at their basal level on transcription of pluripotency factors
c6	0.05	decay rate for pluripotency factors
c7*	1	basal transcription level of differentiation factors
c8	0.001	inhibition constant for transcription of differentiation factors at a basal level of the Oct4-Sox2 complex
c9	0.01	constant of a cooperative inhibitory effect upon an joint impact of Oct4-Sox2 and Nanog proteins at their basal level on transcription of differentiation factors
c10	0.01	decay rate for differentiation factors
q1	0.01	maximal activation constant of Oct4 transcription at a saturating level of the Nanog protein
q2	0.001	activation constant of Oct4 transcription at a basal level of the Nanog protein
q3	0.01	maximal activation constant of Sox2 transcription at a saturating level of the Nanog protein
q4	0.001	activation constant of Sox2 transcription at a basal level of the Nanog protein
p1	1	effective dissociation constant between the Nanog protein and the promoter of the Oct4 gene
h1	2	Hill coefficient for Oct4 transcription regulation by the Nanog protein
p2	1	effective dissociation constant between the Nanog protein and the promoter of the Sox2 gene
h2	2	Hill coefficient for Sox2 transcription regulation by the Nanog protein

* assumption that a transcription rate for the factor is the constant and equals to 1.