Complex_association_c
Complex_association_c
p65_cytoplasm + IkBa_cytoplasm = s19
Complex_degradation_IkBa_c
Complex_degradation_IkBa_c
s19 > p65_cytoplasm
Complex_degradation_IkBa_n
Complex_degradation_IkBa_n
p65_IkBa_nucleus > p65_nucleus
Complex_degradation_p65_c
Complex_degradation_p65_c
s19 > IkBa_cytoplasm
Complex_degradation_p65_n
Complex_degradation_p65_n
p65_IkBa_nucleus > s11
Complex_nuclear_shuttle
Complex_nuclear_shuttle
p65_IkBa_nucleus = s19
IKK_phosphorylation
IKK_phosphorylation
s14 > s15
IkBa_degradation_c
IkBa_degradation_c
IkBa_cytoplasm > ∅
IkBa_degradation_n
IkBa_degradation_n
s11 > ∅
IkBa_mRNA_degradation_c
IkBa_mRNA_degradation_c
IkBa_mRNA_cytoplasm > ∅
IkBa_mRNA_degradation_n
IkBa_mRNA_degradation_n
IkBa_mRNA_nucleus > ∅
IkBa_mRNA_transport
IkBa_mRNA_transport
IkBa_mRNA_nucleus > IkBa_mRNA_cytoplasm
IkBa_nuclear_shuttle
IkBa_nuclear_shuttle
IkBa_cytoplasm = s11
IkBa_phosphorylation
IkBa_phosphorylation
IkBa_cytoplasm > s5
IkBa_transcription_elongation_1
IkBa_transcription_elongation_1
IkBa_pre_mRNA_1 > IkBa_pre_mRNA_2
IkBa_transcription_elongation_2
IkBa_transcription_elongation_2
IkBa_pre_mRNA_2 > IkBa_mRNA_nucleus
IkBa_translation
IkBa_translation
IkBa_mRNA_cytoplasm > IkBa_mRNA_cytoplasm + IkBa_cytoplasm
JNK_active_phosphorylation
JNK_active_phosphorylation
JNK > JNK_P
JNK_basal_phosphorylation
JNK_basal_phosphorylation
JNK > JNK_P
JNK_dephosphorylation
JNK_dephosphorylation
JNK_P > JNK
LPS_LSEC_degradation
LPS_LSEC_degradation
LPS > ∅
LPS_MC_degradation
LPS_MC_degradation
LPS > ∅
MSK1_activation
MSK1_activation
MSK1 > MSK1_P
MSK1_deactivation
MSK1_deactivation
MSK1_P > MSK1
TNFR1_shuttle
TNFR1_shuttle
TNFR1_cytoplasm = TNFR1_EL
TNFa_LSEC_transcription_elongation
TNFa_LSEC_transcription_elongation
TNFa_pre_mRNA_LSEC > TNFa_mRNA_LSEC
TNFa_LSEC_transcription_initiation
TNFa_LSEC_transcription_initiation
∅ > {2.0}TNFa_pre_mRNA_LSEC
TNFa_LSEC_translation
TNFa_LSEC_translation
TNFa_mRNA_LSEC > TNFa_mRNA_LSEC + s16
TNFa_MC_transcription_elongation
TNFa_MC_transcription_elongation
TNFa_pre_mRNA_MC > TNFa_mRNA_MC
TNFa_MC_transcription_initiation
TNFa_MC_transcription_initiation
∅ > {2.0}TNFa_pre_mRNA_MC
TNFa_MC_translation
TNFa_MC_translation
TNFa_mRNA_MC > TNFa_mRNA_MC + s16
TNFa_TNFR1_association
TNFa:TNFR1_association
TNFR1_EL + s16 = TNFa_TNFR1_EL
TNFa_TNFR1_internalisation
TNFa:TNFR1_internalisation
TNFa_TNFR1_EL > TNFa_TNFR1_cytoplasm
TNFa_degradation
TNFa degradation
s16 > ∅
TNFa_internal_degradation
TNFa_internal_degradation
TNFa_TNFR1_cytoplasm > TNFR1_cytoplasm
TNFa_mRNA_LSEC_degradation
TNFa_mRNA_LSEC_degradation
TNFa_mRNA_LSEC > ∅
TNFa_mRNA_MC_degradation
TNFa_mRNA_MC_degradation
TNFa_mRNA_MC > ∅
basal_IKKb_phosphorylation
basal_IKKb_phosphorylation
s14 > s15
p38_active_phosphorylation
p38_active_phosphorylation
p38 > p38_P
p38_basal_phosphorylation
p38_basal_phosphorylation
p38 > p38_P
p38_dephosphorylation
p38_dephosphorylation
p38_P > p38
p65_2P_degradation
p65_2P_degradation
p65_2P > ∅
p65_2P_dephosphorylation_0
p65_2P_dephosphorylation
p65_2P > p65_nucleus
p65_P_degradation_c
p65_P_degradation_c
s3 > ∅
p65_P_degradation_n
p65_P_degradation_n
s8 > ∅
p65_P_dephosphorylation_c
p65_P_dephosphorylation_c
s8 > p65_nucleus
p65_P_dephosphorylation_n
p65_P_dephosphorylation_n
s3 > p65_cytoplasm
p65_P_phosphorylation_MSK1
p65_P_phosphorylation_MSK1
s8 > p65_2P
p65_nuclear_shuttle
p65_nuclear_shuttle
p65_cytoplasm = p65_nucleus
p65_phosphorylation_MSK1
p65_phosphorylation_MSK1
p65_nucleus > p65_2P
p65_translation
p65_translation
p65_mRNA > p65_mRNA + p65_cytoplasm
re10
IkBa_transcription_initiation
∅ > IkBa_pre_mRNA_1
re14
IkBa_p_active_degradation
s5 > ∅
re15
Complex_phosphorylation
s19 > s3 + s5
re17
dephosphorylation IKK
s15 > s14
re19
Complex_association_n
p65_nucleus + s11 = p65_IkBa_nucleus
re3
p65_P_nuclear_shuttle
s3 = s8
Assignment rules
p65_2P_dephosphorylation = p65_P_dephosphorylation_k * 1.0
p65_nuclear_export_k = p65_nuclear_import_k * 0.02
p38_active_phosphorylation_vmax = p38_active_phosphorylation_kcat * TNFa_TNFR1_EL
unscaled_IkBa_P = s5 * default
p65_P_MSK1_phosphrylation_kcat = p65_MSK1_phosphrylation_kcat * 1.0
p65_P_MSK1_phosphrylation_vmax = p65_P_MSK1_phosphrylation_kcat * MSK1_P
MSK1_activation_vmax = MSK1_phosphorylation_kcat * p38_P
p65_P_MSK1_phosphrylation_kM = p65_MSK1_phosphorylation_kM * 1.0
IkBa_p65_phosphorylation_vmax = IkBa_p65_phosphorylation_kcat * s15
unscaled_MSK_P = c1 * MSK1_P
scaled_MSK_P = k_MSK_P * unscaled_MSK_P
scaled_p38_P = k_p38_P * unscaled_p38_P
unscaled_JNK_P = default * JNK_P
scaled_JNK_P = k_JNK_P * unscaled_JNK_P
scaled_IkBa = k_IkBa * unscaled_IkBa
unscaled_p65 = (s3 + s19 + p65_cytoplasm) * default + c1 * (s8 + p65_IkBa_nucleus + p65_nucleus + p65_2P)
k_TNFa_TNFR1_dissociation = k_TNFa_TNFR1_association * 1.9e-5
IkBa_phosphorylation_vmax = IkBa_phosphorylation_kcat * s15
IkBa_phosphorylation_kcat = IkBa_p65_phosphorylation_kcat
unscaled_p65_P = c1 * s8 + default * s3
scaled_p65 = k_p65 * unscaled_p65
IkBa_nuclear_export_k = IkBa_nuclear_import_k * 0.5
scaled_IkBa_P = k_IkBa_P * unscaled_IkBa_P
scaled_IkBa_mRNA = k_IkBa_mRNA * unscaled_IkBa_mRNA
scaled_p65_P = k_p65_P * unscaled_p65_P
IkBa_p65_dissociation_k = IkBa_p65_association_k * 0.003
unscaled_IkBa_mRNA = IkBa_mRNA_cytoplasm * default + c1 * IkBa_mRNA_nucleus
unscaled_p38_P = default * p38_P
p65_MSK1_phosphrylation_vmax = p65_MSK1_phosphrylation_kcat * MSK1_P
unscaled_IkBa = (s11 + p65_IkBa_nucleus) * c1 + (s5 + s19 + IkBa_cytoplasm) * default
JNK_active_phosphorylation_vmax = JNK_active_phosphorylation_kcat * TNFa_TNFR1_EL
Function definitions
Henri_Michaelis_Menten__irreversible(substrate, Km, V) = V * substrate / (Km + substrate)
activated_Transcription__1(k1, k2, Modifier, k3, Modifier2, Modifier3, k4) = k1 + k2 * Modifier + k3 * Modifier2 + k4 * Modifier3
TNFa_transcription_initiation(kbasal, vA, A, kA) = kbasal + vA * A / (A + kA)
Catalytic_activation__irrev(substrate, Activator, Kms, V, Ka) = V * substrate * Activator / ((Kms + substrate) * (Ka + Activator))
Note that constraints are not enforced in simulations. It remains the responsibility of the user to verify that simulation results satisfy these constraints.
No manuscript information is available for this model.
No additional notes are available for this model.