BioModels Database logo

BioModels Database

spacer

BIOMD0000000201 - Goldbeter2008_Somite_Segmentation_Clock_Notch_Wnt_FGF

 

 |   |   |  Send feedback
Reference Publication
Publication ID: 18308339
Goldbeter A, Pourquié O.
Modeling the segmentation clock as a network of coupled oscillations in the Notch, Wnt and FGF signaling pathways.
J. Theor. Biol. 2008 Jun; 252(3): 574-585
Faculté des Sciences, Université Libre de Bruxelles, Campus Plaine, C.P. 231, B-1050 Brussels, Belgium. agoldbet@ulb.ac.be  [more]
Model
Original Model: CellML logo
Submitter: Lukas Endler
Submission ID: MODEL6415057828
Submission Date: 11 Nov 2008 14:56:42 UTC
Last Modification Date: 05 Jun 2013 17:17:15 UTC
Creation Date: 07 Nov 2008 15:03:43 UTC
Encoders:  Catherine Lloyd
   Lukas Endler
set #1
bqbiol:hasVersion Reactome REACT_9470.2
Reactome REACT_299.2
Reactome REACT_11045.1
set #2
bqbiol:hasVersion KEGG Pathway ko04010
KEGG Pathway ko04310
KEGG Pathway ko04330
set #3
bqbiol:isPartOf Gene Ontology somitogenesis
set #4
bqbiol:hasVersion Gene Ontology Wnt signaling pathway
Gene Ontology fibroblast growth factor receptor signaling pathway
Gene Ontology Notch signaling pathway
set #5
bqbiol:occursIn Taxonomy Amniota
Notes

This is a model of the coupled Natch, Wnt and FGF modules as described in:
A. Goldbeter and O. Pourquié , Modeling the segmentation clock as a network of coupled oscillations in the Notch, Wnt and FGF signaling pathways. J Theor Biol. 2008 Jun 7;252(3):574-85, pubmed ID: 18308339
To uncouple the modules remove the reaction MAx_trans_Xa and set vsFK=vsF .
The SBML version of the model was converted from the CellML version by Catherine Lloyd for the CellML repository .


To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.


To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Model
Publication ID: 18308339 Submission Date: 11 Nov 2008 14:56:42 UTC Last Modification Date: 05 Jun 2013 17:17:15 UTC Creation Date: 07 Nov 2008 15:03:43 UTC
Mathematical expressions
Reactions
Notch_synthesis N_degradation Notch_activation Na_degradation
Na_transport Nan_degradation MF_transkription MF_degradation
F_translation F_degradation AK_dissoc B_synth
B_degradation B_phosphorylation BP_dephosphorylation B_shuttling
Bp_degradation MAx_trans_basal MAx_trans_BN MAx_trans_Xa
MAx_degradation A_translation A_degradation Ras_activation
Ras_inactivation Erk_activation Erk_inactivation X_activation
X_inactivation MDusp_transkription MDusp_degradation Dusp_translation
Dusp_degradation      
Rules
Assignment Rule (variable: vsFK) Assignment Rule (variable: Axin2/Gsk3 destruction complex) Assignment Rule (variable: inactive Ras) Assignment Rule (variable: inactive ERK)
Assignment Rule (variable: inactive TF X)      
Physical entities
Compartments Species
cytosol Notch protein cytosolic NicD nuclear NicD
Lunatic fringe mRNA Lunatic Fringe protein phosph. beta-catenin
nuclear beta-catenin Axin2 protein Gsk3
beta-catenin Axin2 mRNA active Ras
active ERK active TF X Dusp6 mRNA
Dusp6 protein inactive Ras inactive ERK
inactive TF X Ras total ERK total
X total Dsh protein Axin2/Gsk3 destruction complex
Kt Fgf  
Global parameters
KdN vsN vdN KdNa
VdNa kt1 kt2 KdNan
VdNan KdMF KIG1 vsFK
vsF vmF KA KdF
vdF ksF kd1 vsB
kd2 v0 vMB vmd
KaB KaXa Kmd n
m vMXa ksAx vdAx
KdAx d1 a1 K1
K2 kt3 kt4 ksDusp
vdDusp KdDusp kcDusp KaFgf
KaRas KdRas KdErk KaErk
KaX KIF KID KdX
KaMDusp KdMDusp q r
kc j p epsilon
theta eta VMsMDusp VMdMDusp
VMK VMP VMaRas VMdRas
VMaErk VMaX VMdX  
Reactions (33)
 
 Notch_synthesis  → [Notch protein];  
 
 N_degradation [Notch protein] → ;  
 
 Notch_activation [Notch protein] → [cytosolic NicD];   {Lunatic Fringe protein}
 
 Na_degradation [cytosolic NicD] → ;  
 
 Na_transport [cytosolic NicD] ↔ [nuclear NicD];  
 
 Nan_degradation [nuclear NicD] → ;  
 
 MF_transkription  → [Lunatic fringe mRNA];   {nuclear NicD}
 
 MF_degradation [Lunatic fringe mRNA] → ;  
 
 F_translation  → [Lunatic Fringe protein];   {Lunatic fringe mRNA}
 
 F_degradation [Lunatic Fringe protein] → ;  
 
 AK_dissoc [Axin2/Gsk3 destruction complex] ↔ [Axin2 protein] + [Gsk3];  
 
 B_synth  → [beta-catenin];  
 
 B_degradation [beta-catenin] → ;  
 
 B_phosphorylation [beta-catenin] → [phosph. beta-catenin];   {Axin2/Gsk3 destruction complex} , {Dsh protein} , {Kt}
 
 BP_dephosphorylation [phosph. beta-catenin] → [beta-catenin];  
 
 B_shuttling [nuclear beta-catenin] ↔ [beta-catenin];  
 
 Bp_degradation [phosph. beta-catenin] → ;  
 
 MAx_trans_basal  → [Axin2 mRNA];   {nuclear beta-catenin}
 
 MAx_trans_BN  → [Axin2 mRNA];   {nuclear beta-catenin}
 
 MAx_trans_Xa  → [Axin2 mRNA];   {active TF X}
 
 MAx_degradation [Axin2 mRNA] → ;  
 
 A_translation  → [Axin2 protein];   {Axin2 mRNA}
 
 A_degradation [Axin2 protein] → ;  
 
 Ras_activation  → [active Ras];   {inactive Ras} , {Fgf}
 
 Ras_inactivation [active Ras] → ;  
 
 Erk_activation  → [active ERK];   {inactive ERK} , {active Ras} , {Ras total}
 
 Erk_inactivation [active ERK] → ;   {Dusp6 protein}
 
 X_activation  → [active TF X];   {active ERK} , {ERK total} , {inactive TF X}
 
 X_inactivation [active TF X] → ;  
 
 MDusp_transkription  → [Dusp6 mRNA];   {active TF X}
 
 MDusp_degradation [Dusp6 mRNA] → ;  
 
 Dusp_translation  → [Dusp6 protein];   {Dusp6 mRNA}
 
 Dusp_degradation [Dusp6 protein] → ;  
 
Rules (5)
 
 Assignment Rule (name: vsFK) vsFK = vsF*KIG1/(KIG1+K)
 
 Assignment Rule (name: AK) Axin2/Gsk3 destruction complex = Kt-K
 
 Assignment Rule (name: Rasi) inactive Ras = Rast-Rasa
 
 Assignment Rule (name: ERKi) inactive ERK = ERKt-ERKa
 
 Assignment Rule (name: Xi) inactive TF X = Xt-Xa
 
  Spatial dimensions: 3.0  Compartment size: 1.0  (Units: litre)
 
 Notch protein
Compartment: cytosol
Initial concentration: 0.5
 
 cytosolic NicD
Compartment: cytosol
Initial concentration: 0.2
 
 nuclear NicD
Compartment: cytosol
Initial concentration: 0.0
 
 Lunatic fringe mRNA
Compartment: cytosol
Initial concentration: 0.1
 
 Lunatic Fringe protein
Compartment: cytosol
Initial concentration: 0.0010
 
 phosph. beta-catenin
Compartment: cytosol
Initial concentration: 0.1
 
 nuclear beta-catenin
Compartment: cytosol
Initial concentration: 0.0010
 
 Axin2 protein
Compartment: cytosol
Initial concentration: 0.1
 
 Gsk3
Compartment: cytosol
Initial concentration: 3.0
 
 beta-catenin
Compartment: cytosol
Initial concentration: 0.1
 
 Axin2 mRNA
Compartment: cytosol
Initial concentration: 0.1
 
 active Ras
Compartment: cytosol
Initial concentration: 0.5
 
 active ERK
Compartment: cytosol
Initial concentration: 0.2
 
 active TF X
Compartment: cytosol
Initial concentration: 0.1
 
 Dusp6 mRNA
Compartment: cytosol
Initial concentration: 0.1
 
 Dusp6 protein
Compartment: cytosol
Initial concentration: 0.1
 
  inactive Ras
Compartment: cytosol
 
  inactive ERK
Compartment: cytosol
 
  inactive TF X
Compartment: cytosol
 
 Ras total
Compartment: cytosol
Initial concentration: 2.0
 
 ERK total
Compartment: cytosol
Initial concentration: 2.0
 
 X total
Compartment: cytosol
Initial concentration: 2.0
 
 Dsh protein
Compartment: cytosol
Initial concentration: 2.0
 
  Axin2/Gsk3 destruction complex
Compartment: cytosol
 
 Kt
Compartment: cytosol
Initial concentration: 3.0
Constant
 
 Fgf
Compartment: cytosol
Initial concentration: 1.0
Constant
 
Global Parameters (71)
 
 KdN
Value: 1.4   (Units: nanomolar)
Constant
 
 vsN
Value: 0.23   (Units: flux)
Constant
 
 vdN
Value: 2.82   (Units: flux)
Constant
 
 KdNa
Value: 0.0010   (Units: nanomolar)
Constant
 
 VdNa
Value: 0.01   (Units: flux)
Constant
 
 kt1
Value: 0.1   (Units: first_order_rate_constant)
Constant
 
 kt2
Value: 0.1   (Units: first_order_rate_constant)
Constant
 
 KdNan
Value: 0.0010   (Units: nanomolar)
Constant
 
 VdNan
Value: 0.1   (Units: flux)
Constant
 
 KdMF
Value: 0.768   (Units: nanomolar)
Constant
 
   KIG1
Value: 2.5   (Units: nanomolar)
Constant
 
  vsFK
Value: NaN   (Units: flux)
 
 vsF
Value: 3.0   (Units: flux)
Constant
 
 vmF
Value: 1.92   (Units: flux)
Constant
 
   KA
Value: 0.05   (Units: nanomolar)
Constant
 
 KdF
Value: 0.37   (Units: nanomolar)
Constant
 
 vdF
Value: 0.39   (Units: flux)
Constant
 
 ksF
Value: 0.3   (Units: first_order_rate_constant)
Constant
 
 kd1
Constant
 
 vsB
Value: 0.087   (Units: flux)
Constant
 
 kd2
Value: 7.062   (Units: first_order_rate_constant)
Constant
 
 v0
Value: 0.06   (Units: flux)
Constant
 
 vMB
Value: 1.64   (Units: flux)
Constant
 
 vmd
Value: 0.8   (Units: flux)
Constant
 
   KaB
Value: 0.7   (Units: nanomolar)
Constant
 
 KaXa
Value: 0.05   (Units: nanomolar)
Constant
 
   Kmd
Value: 0.48   (Units: nanomolar)
Constant
 
 n
Value: 2.0   (Units: dimensionless)
Constant
 
 m
Value: 2.0   (Units: dimensionless)
Constant
 
 vMXa
Value: 0.5   (Units: flux)
Constant
 
 ksAx
Value: 0.02   (Units: first_order_rate_constant)
Constant
 
 vdAx
Value: 0.6   (Units: flux)
Constant
 
 KdAx
Value: 0.63   (Units: nanomolar)
Constant
 
 d1
Value: 0.1   (Units: first_order_rate_constant)
Constant
 
 a1
Value: 1.8   (Units: second_order_rate_constant)
Constant
 
 K1
Value: 0.28   (Units: nanomolar)
Constant
 
 K2
Value: 0.03   (Units: nanomolar)
Constant
 
 kt3
Value: 0.7   (Units: first_order_rate_constant)
Constant
 
 kt4
Value: 1.5   (Units: first_order_rate_constant)
Constant
 
 ksDusp
Value: 0.5   (Units: first_order_rate_constant)
Constant
 
 vdDusp
Value: 2.0   (Units: flux)
Constant
 
 KdDusp
Value: 0.5   (Units: nanomolar)
Constant
 
 kcDusp
Value: 1.35   (Units: first_order_rate_constant)
Constant
 
 KaFgf
Value: 0.5   (Units: nanomolar)
Constant
 
 KaRas
Value: 0.103   (Units: nanomolar)
Constant
 
 KdRas
Value: 0.1   (Units: nanomolar)
Constant
 
 KdErk
Value: 0.05   (Units: nanomolar)
Constant
 
 KaErk
Value: 0.05   (Units: nanomolar)
Constant
 
 KaX
Value: 0.05   (Units: nanomolar)
Constant
 
 KIF
Value: 0.5   (Units: nanomolar)
Constant
 
 KID
Value: 0.5   (Units: nanomolar)
Constant
 
 KdX
Value: 0.05   (Units: nanomolar)
Constant
 
 KaMDusp
Value: 0.5   (Units: nanomolar)
Constant
 
 KdMDusp
Value: 0.5   (Units: nanomolar)
Constant
 
 q
Value: 2.0   (Units: dimensionless)
Constant
 
 r
Value: 2.0   (Units: dimensionless)
Constant
 
 kc
Value: 3.45   (Units: first_order_rate_constant)
Constant
 
 j
Value: 2.0   (Units: dimensionless)
Constant
 
 p
Value: 2.0   (Units: dimensionless)
Constant
 
 epsilon
Value: 0.3   (Units: dimensionless)
Constant
 
 theta
Value: 1.5   (Units: dimensionless)
Constant
 
 eta
Value: 0.3   (Units: dimensionless)
Constant
 
 VMsMDusp
Value: 0.9   (Units: flux)
Constant
 
 VMdMDusp
Value: 0.5   (Units: flux)
Constant
 
 VMK
Value: 5.08   (Units: flux)
Constant
 
 VMP
Value: 1.0   (Units: flux)
Constant
 
 VMaRas
Value: 4.968   (Units: flux)
Constant
 
 VMdRas
Value: 0.41   (Units: flux)
Constant
 
 VMaErk
Value: 3.3   (Units: flux)
Constant
 
 VMaX
Value: 1.6   (Units: flux)
Constant
 
 VMdX
Value: 0.5   (Units: flux)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000201

Curator's comment: (updated: 11 Nov 2008 14:56:24 GMT)

reproduction of fig 4 using SBML odeSolver and xmgrace

spacer
spacer