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BIOMD0000000208 - Deineko2003_CellCycle

 

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Reference Publication
Publication ID: 14582399
Deĭneko IV, Kel' AE, Kel'-Margulis OV, Wingender E, Ratner VA.
[Modeling dynamics of gene net, regulating the cell cycle in mammalian cells]
Genetika 2003 Sep; 39(9): 1285-1292
Institute of Cytology and Genetics, Siberian Division, Russian Academy of Sciences, Novosibirsk, 630090 Russia.  [more]
Model
Original Model: BIOMD0000000208.origin
Submitter: Harish Dharuri
Submission ID: MODEL1475866846
Submission Date: 27 Nov 2008 21:20:03 UTC
Last Modification Date: 05 Jul 2012 14:41:04 UTC
Creation Date: 13 Sep 2008 05:21:44 UTC
Encoders:  Harish Dharuri
set #1
bqbiol:isVersionOf KEGG Pathway Cell cycle - Homo sapiens (human)
Gene Ontology mitotic cell cycle
bqbiol:occursIn Taxonomy Mammalia
Notes

The model reproduces Fig 3 of the paper corresponding to the transition to S phase. Units have not been defined for this model because the paper mentions the use of arbitrary units for the various species and parameters. Model reproduced using MathSBML.


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: 14582399 Submission Date: 27 Nov 2008 21:20:03 UTC Last Modification Date: 05 Jul 2012 14:41:04 UTC Creation Date: 13 Sep 2008 05:21:44 UTC
Mathematical expressions
Reactions
R1 R2 R3 R4
R5 R6 R7 R8
R9 R10 R11 R12
R13 R14 R15  
Rules
Assignment Rule (variable: F6)      
Physical entities
Compartments Species
compartment E2F pRB Phosphorylated pRB
inactive cycE_cdk2 active cycE_cdk2 AP-1
Global parameters
emax k1 k1_prime k1_double_prime
phi1 k2 k3 phi2
phi3 k4 k4_double_prime k4i
k4a phi4i phi4a k6
F6 phi6    
Reactions (15)
 
 R1  → [E2F];   {pRB}
 
 R2 [E2F] → ;  
 
 R3  → [pRB];   {E2F}
 
 R4 [pRB] → [Phosphorylated pRB];   {active cycE_cdk2}
 
 R5 [pRB] → ;  
 
 R6 [Phosphorylated pRB] → ;  
 
 R7  → [inactive cycE_cdk2];   {E2F}
 
 R8  → [inactive cycE_cdk2];   {AP-1}
 
 R9 [inactive cycE_cdk2] → [active cycE_cdk2];  
 
 R10 [active cycE_cdk2] → [inactive cycE_cdk2];  
 
 R11 [inactive cycE_cdk2] → ;  
 
 R12 [active cycE_cdk2] → ;  
 
 R13  → [AP-1];   {E2F}
 
 R14  → [AP-1];  
 
 R15 [AP-1] → ;  
 
Rules (1)
 
 Assignment Rule (name: F6) F6 = piecewise(0.044, t <= 60, 0)
 
   Spatial dimensions: 3.0  Compartment size: 1.0
 
 E2F
Compartment: compartment
Initial concentration: 0.014
 
 pRB
Compartment: compartment
Initial concentration: 0.0060
 
 Phosphorylated pRB
Compartment: compartment
Initial concentration: 0.0
 
 inactive cycE_cdk2
Compartment: compartment
Initial concentration: 0.0
 
 active cycE_cdk2
Compartment: compartment
Initial concentration: 1.0E-4
 
 AP-1
Compartment: compartment
Initial concentration: 0.0
 
Global Parameters (18)
 
   emax
Value: 2.0
Constant
 
   k1
Value: 1.0
Constant
 
   k1_prime
Value: 1.0
Constant
 
   k1_double_prime
Value: 10.0
Constant
 
   phi1
Value: 0.1
Constant
 
   k2
Value: 1.0
Constant
 
   k3
Value: 0.4
Constant
 
   phi2
Value: 0.01
Constant
 
   phi3
Value: 0.1
Constant
 
   k4
Value: 0.09
Constant
 
   k4_double_prime
Value: 0.1
Constant
 
   k4i
Value: 1.0
Constant
 
   k4a
Value: 2.0
Constant
 
   phi4i
Value: 0.01
Constant
 
   phi4a
Value: 0.01
Constant
 
   k6
Constant
 
   F6
Value: 0.044
 
   phi6
Value: 0.1
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000208

Curator's comment: (updated: 27 Nov 2008 21:19:47 GMT)

Plot corresponds to Fig 3a of the paper. MathSBML was used to simulate the model.

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