BioModels Database logo

BioModels Database

spacer

BIOMD0000000250 - Nakakuki2010_CellFateDecision_Mechanistic

 

 |   |   |  Send feedback
Reference Publication
Publication ID: 20493519
Nakakuki T, Birtwistle MR, Saeki Y, Yumoto N, Ide K, Nagashima T, Brusch L, Ogunnaike BA, Okada-Hatakeyama M, Kholodenko BN.
Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics.
Cell 2010 May; 141(5): 884-896
Computational Systems Biology Research Group, Advanced Computational Sciences Department, RIKEN Advanced Science Institute, 1-7-22 Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.  [more]
Model
Original Model: Nakakuki et al., Ligand-sp...
Submitter: Lutz Brusch
Submission ID: MODEL1004300000
Submission Date: 30 Apr 2010 20:00:20 UTC
Last Modification Date: 28 Feb 2014 16:00:47 UTC
Creation Date: 30 Apr 2010 11:41:28 UTC
Encoders:  Lukas Endler
set #1
bqmodel:isDerivedFrom BioModels Database Birtwistle2007_ErbB_Signalling
PubMed 12242336
set #2
bqbiol:isVersionOf Gene Ontology epidermal growth factor receptor signaling pathway via MAPK cascade
Gene Ontology obsolete MAPKKK cascade involved in epidermal growth factor receptor signaling
set #3
bqbiol:occursIn Brenda Tissue Ontology MCF-7 cell
set #4
bqbiol:isVersionOf Reactome REACT_9417
set #5
bqbiol:hasVersion Reactome REACT_634
set #6
bqbiol:isPartOf KEGG Pathway MAPK signaling pathway - Homo sapiens (human)
set #7
bqbiol:hasTaxon Taxonomy Homo sapiens
Notes

This mechanistic model describes the activation of immediate early genes such as cFos after EGF or heregulin (HRG) stimulation of the MAPK pathway. Phosphorylated cFos is a key transcription factor triggering downstream cascades of cell fate determination. The model can explain how the switch-like response of p-cFos emerges from the spatiotemporal dynamics. This mechanistic model comprises the explicit reaction kinetics of the signal transduction pathway, the transcriptional and the posttranslational feedback and feedforward loops. In the below article, two different mechanistic models have been studied, the first one based on previously known interactions but failing to account for the experimental data and the second one including additional interactions which were discovered and confirmed by new experiments. The mechanistic model encoded here is the second one, the extended and at the time of creation most complete model of cell fate decision making in response to different doses of EGF or HRG stimulation. The encoded parameter set corresponds to 10mM HRG stimulation as shown in Fig.1 of the article. The Supplementary Methods of the article provide further parameter sets that allow simulations for different ligands and different doses. A corresponding core model is available from http://www.ebi.ac.uk/biomodels/ as MODEL1003170000.

Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics.
Takashi Nakakuki(1), Marc R. Birtwistle(2,3,4), Yuko Saeki(1,5), Noriko Yumoto(1,5), Kaori Ide(1), Takeshi Nagashima(1,5), Lutz Brusch(6), Babatunde A. Ogunnaike(3), Mariko Hatakeyama(1,5), and Boris N. Kholodenko(2,4); Cell In Press, online 20 May 2010 , doi: 10.1016/j.cell.2010.03.054
(1) RIKEN Advanced Science Institute, Computational Systems Biology Research Group, Advanced Computational Sciences Department, 1-7-22 Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
(2) Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
(3) University of Delaware, Department of Chemical Engineering, 150 Academy St., Newark, DE 19716, USA
(4) Thomas Jefferson University, Department of Pathology, Anatomy, and Cell Biology, 1020 Locust Street, Philadelphia, PA 19107, USA
(5) RIKEN Research Center for Allergy and Immunology, Laboratory for Cellular Systems Modeling, 1-7-22 Tsurumi-ku, Yokohama, 230-0045, Japan
(6) Dresden University of Technology, Center for Information Services and High Performance Computing, 01062 Dresden, Germany

Model
Publication ID: 20493519 Submission Date: 30 Apr 2010 20:00:20 UTC Last Modification Date: 28 Feb 2014 16:00:47 UTC Creation Date: 30 Apr 2010 11:41:28 UTC
Mathematical expressions
Reactions
v001 v002 v003 v004
v005 v006 v007 v008
v009 v010 v011 v012
v013 v014 v015 v016
v017 v018 v019 v020
v021 v022 v023 v024
v025 v026 v027 v028
v029 v030 v031 v032
v033 v034 v035 v036
v037 v038 v039 v040
v041 v042 v043 v044
v045 v046 v047 v048
v049 v050 v051 v052
v053 v054 v055 v056
v057 v058 v059 v060
v061 v062 v063 v101
v102 v103 v104 v105
v106 v107 v108 v109
v110 v111 v112 v113
v114 v115    
Physical entities
Compartments Species
default EGF HRG  
cytoplasm A1 A1_2 A2
A2_2 A3 A3_2
DUSPmRNA ERK_c pERK_c
ppERK_c F c_FOS_c
pc_FOS_c c_FOSmRNA FmRNA
Kin Kin_2 pMEK
MEK DUSP_c pDUSP_c
RSK_c pRSK_c RsD
RsT    
nucleus CREB_n pCREB_n ERK_n
pERK_n ppERK_n Elk1_n
pElk1_n FOSn FOSn_2
Fn DUSP_n pDUSP_n
pDUSP_n_ERK_n pDUSP_n_pERK_n pDUSP_n_ppERK_n
DUSP_n_ERK_n DUSP_n_pERK_n DUSP_n_ppERK_n
PreDUSPmRNA PreFOSmRNA PreFmRNA
pRSK_n    
Global parameters
V2 V3 K3 V4
K4 V5 K5 V6
K6 KimERK KexERK KimERKP
KexERKP KimERKPP KexERKPP V10
K10 n10 p11 p12
p13 V14 K14 V15
K15 p16 p17 KimDUSP
KexDUSP KimDUSPP KexDUSPP V20
K20 V21 K21 p22
p23 V24 K24 V1
K1 V25 K25 KimRSKP
KexRSKP V27 K27 V28
K28 V29 K29 V30
K30 V31 K31 n31
p32 p33 p34 V35
K35 V36 K36 V37
K37 p38 p39 KimFOS
KexFOS KimFOSP KexFOSP V42
K42 V43 K43 V44
K44 p45 p46 p47
m47 p48 p49 m49
p50 p51 m51 Fct
p52 m52 p53 p54
m54 p55 p56 m56
V57 K57 n57 p58
p59 p60 p61 KimF
KexF p63 KF31 nF31
K2 Vn Vc V101
K101 V102 K102 V103
K103 V104 K104 V105
K105 V106 K106 V107
K107 V108 K108 V109
K109 V110 K110 V111
K111 V112 K112 V113
K113 V114 K114 V115
K115      
Reactions (78)
 
 v001 [ERK_c] → [pERK_c];   {pMEK} , {pERK_c}
 
 v002 [pERK_c] → [ppERK_c];   {pMEK} , {ERK_c}
 
 v003 [pERK_c] → [ERK_c];   {ppERK_c}
 
 v004 [ppERK_c] → [pERK_c];   {pERK_c}
 
 v005 [pERK_n] → [ERK_n];   {ppERK_n}
 
 v006 [ppERK_n] → [pERK_n];   {pERK_n}
 
 v007 [ERK_c] ↔ [ERK_n];  
 
 v008 [pERK_c] ↔ [pERK_n];  
 
 v009 [ppERK_c] ↔ [ppERK_n];  
 
 v010  → [PreDUSPmRNA];   {ppERK_n}
 
 v011 [PreDUSPmRNA] → [DUSPmRNA];  
 
 v012 [DUSPmRNA] → ;  
 
 v013  → [DUSP_c];   {DUSPmRNA}
 
 v014 [DUSP_c] → [pDUSP_c];   {ppERK_c}
 
 v015 [pDUSP_c] → [DUSP_c];  
 
 v016 [DUSP_c] → ;  
 
 v017 [pDUSP_c] → ;  
 
 v018 [DUSP_c] ↔ [DUSP_n];  
 
 v019 [pDUSP_c] ↔ [pDUSP_n];  
 
 v020 [DUSP_n] → [pDUSP_n];   {ppERK_n}
 
 v021 [pDUSP_n] → [DUSP_n];  
 
 v022 [DUSP_n] → ;  
 
 v023 [pDUSP_n] → ;  
 
 v024 [RSK_c] → [pRSK_c];   {ppERK_c}
 
 v025 [pRSK_c] → [RSK_c];  
 
 v026 [pRSK_c] ↔ [pRSK_n];  
 
 v027 [CREB_n] → [pCREB_n];   {pRSK_n}
 
 v028 [pCREB_n] → [CREB_n];  
 
 v029 [Elk1_n] → [pElk1_n];   {ppERK_n}
 
 v030 [pElk1_n] → [Elk1_n];  
 
 v031  → [PreFOSmRNA];   {pCREB_n} , {pElk1_n} , {Fn}
 
 v032 [PreFOSmRNA] → [c_FOSmRNA];  
 
 v033 [c_FOSmRNA] → ;  
 
 v034  → [c_FOS_c];   {c_FOSmRNA}
 
 v035 [c_FOS_c] → [pc_FOS_c];   {ppERK_c}
 
 v036 [c_FOS_c] → [pc_FOS_c];   {pRSK_c}
 
 v037 [pc_FOS_c] → [c_FOS_c];  
 
 v038 [c_FOS_c] → ;  
 
 v039 [pc_FOS_c] → ;  
 
 v040 [c_FOS_c] ↔ [FOSn];  
 
 v041 [pc_FOS_c] ↔ [FOSn_2];  
 
 v042 [FOSn] → [FOSn_2];   {ppERK_n}
 
 v043 [FOSn] → [FOSn_2];   {pRSK_n}
 
 v044 [FOSn_2] → [FOSn];  
 
 v045 [FOSn] → ;  
 
 v046 [FOSn_2] → ;  
 
 v047 [pDUSP_n] + [ppERK_n] ↔ [pDUSP_n_ppERK_n];  
 
 v048 [pDUSP_n_ppERK_n] → [pDUSP_n] + [pERK_n];  
 
 v049 [pDUSP_n] + [pERK_n] ↔ [pDUSP_n_pERK_n];  
 
 v050 [pDUSP_n_pERK_n] → [pDUSP_n] + [ERK_n];  
 
 v051 [pDUSP_n] + [ERK_n] ↔ [pDUSP_n_ERK_n];  
 
 v052 [DUSP_n] + [ppERK_n] ↔ [DUSP_n_ppERK_n];  
 
 v053 [DUSP_n_ppERK_n] → [DUSP_n] + [pERK_n];  
 
 v054 [DUSP_n] + [pERK_n] ↔ [DUSP_n_pERK_n];  
 
 v055 [DUSP_n_pERK_n] → [DUSP_n] + [ERK_n];  
 
 v056 [DUSP_n] + [ERK_n] ↔ [DUSP_n_ERK_n];  
 
 v057  → [PreFmRNA];   {FOSn_2}
 
 v058 [PreFmRNA] → [FmRNA];  
 
 v059 [FmRNA] → ;  
 
 v060  → [F];   {FmRNA}
 
 v061 [F] → ;  
 
 v062 [F] ↔ [Fn];  
 
 v063 [Fn] → ;  
 
 v101 [A1] → [A1_2];   {EGF}
 
 v102 [A1_2] → [A1];  
 
 v103 [A2] → [A2_2];   {HRG}
 
 v104 [A2_2] → [A2];  
 
 v105 [RsD] → [RsT];   {EGF}
 
 v106 [RsD] → [RsT];   {HRG}
 
 v107 [RsT] → [RsD];   {A1_2}
 
 v108 [RsT] → [RsD];   {A2_2}
 
 v109 [A3] → [A3_2];   {HRG}
 
 v110 [A3_2] → [A3];  
 
 v111 [Kin] → [Kin_2];   {HRG}
 
 v112 [Kin_2] → [Kin];   {A3_2}
 
 v113 [MEK] → [pMEK];   {RsT}
 
 v114 [MEK] → [pMEK];   {Kin_2}
 
 v115 [pMEK] → [MEK];  
 
Functions (56)
 
 function_4_v003 lambda(K3, K4, V3, pERK_c, ppERK_c, V3*pERK_c/(K3*(1+ppERK_c/K4)+pERK_c))
 
 function_4_v004 lambda(K3, K4, V4, pERK_c, ppERK_c, V4*ppERK_c/(K4*(1+pERK_c/K3)+ppERK_c))
 
 function_4_v005 lambda(K5, K6, V5, pERK_n, ppERK_n, V5*pERK_n/(K5*(1+ppERK_n/K6)+pERK_n))
 
 function_4_v006 lambda(K5, K6, V6, pERK_n, ppERK_n, V6*ppERK_n/(K6*(1+pERK_n/K5)+ppERK_n))
 
 function_4_v007 lambda(KexERK, KimERK, Vc, Vn, ERK_c, ERK_n, KimERK*Vc*ERK_c-KexERK*Vn*ERK_n)
 
 function_4_v008 lambda(KexERKP, KimERKP, Vc, Vn, pERK_c, pERK_n, KimERKP*Vc*pERK_c-KexERKP*Vn*pERK_n)
 
 function_4_v015 lambda(K15, V15, pDUSP_c, V15*pDUSP_c/(K15+pDUSP_c))
 
 function_4_v018 lambda(KexDUSP, KimDUSP, Vc, Vn, DUSP_n, DUSP_c, KimDUSP*Vc*DUSP_c-KexDUSP*Vn*DUSP_n)
 
 function_4_v019 lambda(KexDUSPP, KimDUSPP, Vc, Vn, pDUSP_c, pDUSP_n, KimDUSPP*Vc*pDUSP_c-KexDUSPP*Vn*pDUSP_n)
 
 function_4_v020 lambda(K20, V20, ppERK_n, DUSP_n, V20*ppERK_n*DUSP_n/(K20+DUSP_n))
 
 function_4_v021 lambda(K21, V21, pDUSP_n, V21*pDUSP_n/(K21+pDUSP_n))
 
 function_4_v024 lambda(K24, V24, ppERK_c, RSK_c, V24*ppERK_c*RSK_c/(K24+RSK_c))
 
 function_4_v001 lambda(Fct, K1, K2, V1, ERK_c, pERK_c, MEKc, V1*Fct*MEKc*ERK_c/(K1*(1+pERK_c/K2)+ERK_c))
 
 function_4_v009 lambda(KexERKPP, KimERKPP, Vc, Vn, ppERK_c, ppERK_n, KimERKPP*Vc*ppERK_c-KexERKPP*Vn*ppERK_n)
 
 function_4_v010 lambda(K10, V10, n10, ppERK_n, V10*ppERK_n^n10/(K10^n10+ppERK_n^n10))
 
 function_4_v011 lambda(Vn, p11, PreDUSPmRNA, p11*Vn*PreDUSPmRNA)
 
 function_4_v013 lambda(p13, DUSPmRNA, p13*DUSPmRNA)
 
 function_4_v014 lambda(K14, V14, ppERK_c, DUSP_c, V14*ppERK_c*DUSP_c/(K14+DUSP_c))
 
 function_4_v002 lambda(Fct, K1, K2, V2, ERK_c, pERK_c, MEKc, V2*Fct*MEKc*pERK_c/(K2*(1+ERK_c/K1)+pERK_c))
 
 function_4_v029 lambda(K29, V29, ppERK_n, Elk1_n, V29*ppERK_n*Elk1_n/(K29+Elk1_n))
 
 function_4_v025 lambda(K25, V25, pRSK_c, V25*pRSK_c/(K25+pRSK_c))
 
 function_4_v026 lambda(KexRSKP, KimRSKP, Vc, Vn, pRSK_n, pRSK_c, KimRSKP*Vc*pRSK_c-KexRSKP*Vn*pRSK_n)
 
 function_4_v032 lambda(Vn, p32, PreFOSmRNA, p32*Vn*PreFOSmRNA)
 
 function_4_v034 lambda(p34, c_FOSmRNA, p34*c_FOSmRNA)
 
 function_4_v035 lambda(K35, V35, c_FOS_c, ppERK_c, V35*ppERK_c*c_FOS_c/(K35+c_FOS_c))
 
 function_4_v036 lambda(K36, V36, c_FOS_c, pRSK_c, V36*pRSK_c*c_FOS_c/(K36+c_FOS_c))
 
 function_4_v037 lambda(K37, V37, pc_FOS_c, V37*pc_FOS_c/(K37+pc_FOS_c))
 
 function_4_v027 lambda(K27, V27, CREB_n, pRSK_n, V27*pRSK_n*CREB_n/(K27+CREB_n))
 
 function_4_v028 lambda(K28, V28, pCREB_n, V28*pCREB_n/(K28+pCREB_n))
 
 function_4_v030 lambda(K30, V30, pElk1_n, V30*pElk1_n/(K30+pElk1_n))
 
 function_4_v031 lambda(K31, KF31, V31, n31, nF31, Fn, pCREB_n, pElk1_n, V31*(pCREB_n*pElk1_n)^n31/(K31^n31+(pCREB_n*pElk1_n)^n31+(Fn/KF31)^nF31))
 
 function_4_v040 lambda(KexFOS, KimFOS, Vc, Vn, c_FOS_c, FOSn, KimFOS*Vc*c_FOS_c-KexFOS*Vn*FOSn)
 
 function_4_v041 lambda(KexFOSP, KimFOSP, Vc, Vn, pc_FOS_c, FOSn_2, KimFOSP*Vc*pc_FOS_c-KexFOSP*Vn*FOSn_2)
 
 function_4_v042 lambda(K42, V42, ppERK_n, FOSn, V42*ppERK_n*FOSn/(K42+FOSn))
 
 function_4_v043 lambda(K43, V43, FOSn, pRSK_n, V43*pRSK_n*FOSn/(K43+FOSn))
 
 function_4_v044 lambda(K44, V44, FOSn_2, V44*FOSn_2/(K44+FOSn_2))
 
 function_4_v057 lambda(K57, V57, n57, FOSn_2, V57*FOSn_2^n57/(K57^n57+FOSn_2^n57))
 
 function_4_v058 lambda(Vn, p58, PreFmRNA, p58*Vn*PreFmRNA)
 
 function_4_v060 lambda(p60, FmRNA, p60*FmRNA)
 
 function_4_v062 lambda(KexF, KimF, Vc, Vn, F, Fn, KimF*Vc*F-KexF*Vn*Fn)
 
 function_4_v063 lambda(cytoplasm, nucleus, p63, Fn, cytoplasm*p63*Fn/nucleus)
 
 function_4_v101 lambda(K101, V101, A1, EGF, V101*EGF*A1/(K101+A1))
 
 function_4_v102 lambda(K102, V102, A1_2, V102*A1_2/(K102+A1_2))
 
 function_4_v103 lambda(K103, V103, A2, HRG, V103*HRG*A2/(K103+A2))
 
 function_4_v104 lambda(K104, V104, A2_2, V104*A2_2/(K104+A2_2))
 
 function_4_v105 lambda(K105, V105, EGF, RsD, V105*EGF*RsD/(K105+RsD))
 
 function_4_v106 lambda(K106, V106, HRG, RsD, V106*HRG*RsD/(K106+RsD))
 
 function_4_v107 lambda(K107, V107, A1_2, RsT, V107*A1_2*RsT/(K107+RsT))
 
 function_4_v108 lambda(K108, V108, A2_2, RsT, V108*A2_2*RsT/(K108+RsT))
 
 function_4_v109 lambda(K109, V109, HRG, A3, V109*HRG*A3/(K109+A3))
 
 function_4_v110 lambda(K110, V110, A3_2, V110*A3_2/(K110+A3_2))
 
 function_4_v111 lambda(K111, V111, HRG, Kin, V111*HRG*Kin/(K111+Kin))
 
 function_4_v112 lambda(K112, V112, A3_2, Kin_2, V112*A3_2*Kin_2/(K112+Kin_2))
 
 function_4_v113 lambda(K113, V113, RsT, pMEK_c, V113*RsT*pMEK_c/(K113+pMEK_c))
 
 function_4_v114 lambda(K114, V114, Kin_2, pMEK_c, V114*Kin_2*pMEK_c/(K114+pMEK_c))
 
 function_4_v115 lambda(K115, V115, MEKc, V115*MEKc/(K115+MEKc))
 
 default Spatial dimensions: 3.0  Compartment size: 1.0
 
 EGF
Compartment: default
Initial concentration: 0.0
Constant
 
 HRG
Compartment: default
Initial concentration: 10.0
Constant
 
 cytoplasm Spatial dimensions: 3.0  Compartment size: 940.0
 
   A1
Compartment: cytoplasm
Initial concentration: 182.3524
 
   A1_2
Compartment: cytoplasm
Initial concentration: 0.0
 
   A2
Compartment: cytoplasm
Initial concentration: 25.38702
 
   A2_2
Compartment: cytoplasm
Initial concentration: 0.0
 
   A3
Compartment: cytoplasm
Initial concentration: 13.09262
 
   A3_2
Compartment: cytoplasm
Initial concentration: 0.0
 
 DUSPmRNA
Compartment: cytoplasm
Initial concentration: 0.0
 
 ERK_c
Compartment: cytoplasm
Initial concentration: 570.4179
 
 pERK_c
Compartment: cytoplasm
Initial concentration: 0.0
 
 ppERK_c
Compartment: cytoplasm
Initial concentration: 0.0
 
 F
Compartment: cytoplasm
Initial concentration: 0.0
 
 c_FOS_c
Compartment: cytoplasm
Initial concentration: 0.0
 
 pc_FOS_c
Compartment: cytoplasm
Initial concentration: 0.0
 
 c_FOSmRNA
Compartment: cytoplasm
Initial concentration: 0.0
 
 FmRNA
Compartment: cytoplasm
Initial concentration: 0.0
 
 Kin
Compartment: cytoplasm
Initial concentration: 82.66574
 
 Kin_2
Compartment: cytoplasm
Initial concentration: 0.0
 
 pMEK
Compartment: cytoplasm
Initial concentration: 0.0
 
 MEK
Compartment: cytoplasm
Initial concentration: 637.3212
 
 DUSP_c
Compartment: cytoplasm
Initial concentration: 0.0
 
 pDUSP_c
Compartment: cytoplasm
Initial concentration: 0.0
 
 RSK_c
Compartment: cytoplasm
Initial concentration: 353.0
 
 pRSK_c
Compartment: cytoplasm
Initial concentration: 0.0
 
 RsD
Compartment: cytoplasm
Initial concentration: 247.4035
 
 RsT
Compartment: cytoplasm
Initial concentration: 0.0
 
 nucleus Spatial dimensions: 3.0  Compartment size: 220.0
 
 CREB_n
Compartment: nucleus
Initial concentration: 1000.0
 
 pCREB_n
Compartment: nucleus
Initial concentration: 0.0
 
 ERK_n
Compartment: nucleus
Initial concentration: 1624.9
 
 pERK_n
Compartment: nucleus
Initial concentration: 0.0
 
 ppERK_n
Compartment: nucleus
Initial concentration: 0.0
 
 Elk1_n
Compartment: nucleus
Initial concentration: 1510.0
 
 pElk1_n
Compartment: nucleus
Initial concentration: 0.0
 
 FOSn
Compartment: nucleus
Initial concentration: 0.0
 
 FOSn_2
Compartment: nucleus
Initial concentration: 0.0
 
   Fn
Compartment: nucleus
Initial concentration: 0.0
 
 DUSP_n
Compartment: nucleus
Initial concentration: 0.0
 
 pDUSP_n
Compartment: nucleus
Initial concentration: 0.0
 
 pDUSP_n_ERK_n
Compartment: nucleus
Initial concentration: 0.0
 
 pDUSP_n_pERK_n
Compartment: nucleus
Initial concentration: 0.0
 
 pDUSP_n_ppERK_n
Compartment: nucleus
Initial concentration: 0.0
 
 DUSP_n_ERK_n
Compartment: nucleus
Initial concentration: 0.0
 
 DUSP_n_pERK_n
Compartment: nucleus
Initial concentration: 0.0
 
 DUSP_n_ppERK_n
Compartment: nucleus
Initial concentration: 0.0
 
 PreDUSPmRNA
Compartment: nucleus
Initial concentration: 0.0
 
 PreFOSmRNA
Compartment: nucleus
Initial concentration: 0.0
 
 PreFmRNA
Compartment: nucleus
Initial concentration: 0.0
 
 pRSK_n
Compartment: nucleus
Initial concentration: 0.0
 
Global Parameters (141)
 
   V2
Value: 0.22
Constant
 
   V3
Value: 0.72
Constant
 
   K3
Value: 160.0
Constant
 
   V4
Value: 0.648
Constant
 
   K4
Value: 60.0
Constant
 
   V5
Value: 19.49872346
Constant
 
   K5
Value: 29.94073716
Constant
 
   V6
Value: 19.4987234631759
Constant
 
   K6
Value: 29.9407371620698
Constant
 
   KimERK
Value: 0.012
Constant
 
   KexERK
Value: 0.018
Constant
 
   KimERKP
Value: 0.012
Constant
 
   KexERKP
Value: 0.018
Constant
 
   KimERKPP
Value: 0.011
Constant
 
   KexERKPP
Value: 0.013
Constant
 
   V10
Value: 29.24109258
Constant
 
   K10
Value: 169.0473748
Constant
 
   n10
Value: 3.970849295
Constant
 
   p11
Value: 1.26129E-4
Constant
 
   p12
Value: 0.007875765
Constant
 
   p13
Value: 0.001245747
Constant
 
   V14
Value: 5.636949216
Constant
 
   K14
Value: 34180.48
Constant
 
   V15
Value: 2.992346912
Constant
 
   K15
Value: 0.001172165
Constant
 
   p16
Value: 2.57E-4
Constant
 
   p17
Value: 4.81E-5
Constant
 
   KimDUSP
Value: 0.024269764
Constant
 
   KexDUSP
Value: 0.070467899
Constant
 
   KimDUSPP
Value: 0.024269764
Constant
 
   KexDUSPP
Value: 0.070467899
Constant
 
   V20
Value: 0.157678678
Constant
 
   K20
Value: 735598.6967
Constant
 
   V21
Value: 0.005648117
Constant
 
   K21
Value: 387.8377182
Constant
 
   p22
Value: 2.57E-4
Constant
 
   p23
Value: 4.81E-5
Constant
 
   V24
Value: 0.550346114
Constant
 
   K24
Value: 29516.06587
Constant
 
   V1
Value: 0.342848369838443
Constant
 
   K1
Value: 307.041525298866
Constant
 
   V25
Value: 10.09063736
Constant
 
   K25
Value: 0.913939859
Constant
 
   KimRSKP
Value: 0.025925065
Constant
 
   KexRSKP
Value: 0.129803956
Constant
 
   V27
Value: 19.23118154
Constant
 
   K27
Value: 441.5834425
Constant
 
   V28
Value: 6.574759504
Constant
 
   K28
Value: 14.99180922
Constant
 
   V29
Value: 0.518529841
Constant
 
   K29
Value: 21312.69109
Constant
 
   V30
Value: 13.79479021
Constant
 
   K30
Value: 15.04396629
Constant
 
   V31
Value: 0.655214248
Constant
 
   K31
Value: 185.9760682
Constant
 
   n31
Value: 1.988003164
Constant
 
   p32
Value: 0.003284434
Constant
 
   p33
Value: 6.01234209304622E-4
Constant
 
   p34
Value: 7.64816282169636E-5
Constant
 
   V35
Value: 8.907637012
Constant
 
   K35
Value: 8562.744184
Constant
 
   V36
Value: 5.97315E-4
Constant
 
   K36
Value: 528.552427
Constant
 
   V37
Value: 1.745848179
Constant
 
   K37
Value: 0.070379236
Constant
 
   p38
Value: 2.57E-4
Constant
 
   p39
Value: 4.81E-5
Constant
 
   KimFOS
Value: 0.54528521
Constant
 
   KexFOS
Value: 0.133249762
Constant
 
   KimFOSP
Value: 0.54528521
Constant
 
   KexFOSP
Value: 0.133249762
Constant
 
   V42
Value: 0.909968714
Constant
 
   K42
Value: 3992.061328
Constant
 
   V43
Value: 0.076717457
Constant
 
   K43
Value: 1157.116021
Constant
 
   V44
Value: 0.078344305
Constant
 
   K44
Value: 0.051168202
Constant
 
   p45
Value: 2.57E-4
Constant
 
   p46
Value: 4.81E-5
Constant
 
   p47
Value: 0.001670815
Constant
 
   m47
Value: 15.80783969
Constant
 
   p48
Value: 0.686020478
Constant
 
   p49
Value: 0.314470502
Constant
 
   m49
Value: 2.335459127
Constant
 
   p50
Value: 26.59483436
Constant
 
   p51
Value: 0.01646825
Constant
 
   m51
Value: 9.544308421
Constant
 
   Fct
Value: 0.7485
Constant
 
   p52
Value: 0.001670815
Constant
 
   m52
Value: 15.80783969
Constant
 
   p53
Value: 0.686020478
Constant
 
   p54
Value: 0.314470502
Constant
 
   m54
Value: 2.335459127
Constant
 
   p55
Value: 26.59483436
Constant
 
   p56
Value: 0.01646825
Constant
 
   m56
Value: 9.544308421
Constant
 
   V57
Value: 1.026834758
Constant
 
   K57
Value: 0.637490056
Constant
 
   n57
Value: 3.584464176
Constant
 
   p58
Value: 2.70488E-4
Constant
 
   p59
Value: 0.001443889
Constant
 
   p60
Value: 0.002448164
Constant
 
   p61
Value: 3.49860901414122E-5
Constant
 
   KimF
Value: 0.019898797
Constant
 
   KexF
Value: 0.396950616
Constant
 
   p63
Value: 4.13466150826031E-5
Constant
 
   KF31
Value: 0.013844393
Constant
 
   nF31
Value: 2.800340453
Constant
 
   K2
Value: 350.0
Constant
 
   Vn
Value: 220.0
Constant
 
   Vc
Value: 940.0
Constant
 
   V101
Value: 0.01807448
Constant
 
   K101
Value: 3475.168
Constant
 
   V102
Value: 0.09858154
Constant
 
   K102
Value: 237.2001
Constant
 
   V103
Value: 0.3573399
Constant
 
   K103
Value: 1334.132
Constant
 
   V104
Value: 4.635749
Constant
 
   K104
Value: 4046.71
Constant
 
   V105
Value: 0.05393704
Constant
 
   K105
Value: 1.027895
Constant
 
   V106
Value: 0.109304
Constant
 
   K106
Value: 606.871
Constant
 
   V107
Value: 5.291093
Constant
 
   K107
Value: 424.6884
Constant
 
   V108
Value: 0.03436149
Constant
 
   K108
Value: 11.5048
Constant
 
   V109
Value: 0.1374307
Constant
 
   K109
Value: 7424.816
Constant
 
   V110
Value: 0.08258693
Constant
 
   K110
Value: 425.5268
Constant
 
   V111
Value: 0.02487469
Constant
 
   K111
Value: 858.3423
Constant
 
   V112
Value: 0.8850982
Constant
 
   K112
Value: 4665.217
Constant
 
   V113
Value: 0.05377297
Constant
 
   K113
Value: 20.50809
Constant
 
   V114
Value: 0.03957055
Constant
 
   K114
Value: 7.774197
Constant
 
   V115
Value: 13.74244
Constant
 
   K115
Value: 2122.045
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000250

Curator's comment: (updated: 24 May 2010 11:51:19 BST)

Reproduction of fig 1 F-I of the original publication. Integrations were performed using SBML ODESolver. The concentrations were rescaled to the highest level of HRG induced activation.
Fig 1I differs slightly, either due to a different amount of plotting points or differences in the normalization.

spacer
spacer