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BIOMD0000000168 - Obeyesekere1999_CellCycle

 

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Reference Publication
Publication ID: 17886749
Obeyesekere MN, Zimmerman SO, Tecarro ES, Auchmuty G.
A model of cell cycle behavior dominated by kinetics of a pathway stimulated by growth factors.
Bull. Math. Biol. 1999 Sep; 61(5): 917-934
Department of Biomathematics, P. O. Box 237, The University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA. mandri@odin.mdacc.tmc.edu  [more]
Model
Original Model: http://www.itb.cnr.it/cell...
Submitter: Nicolas Le Novère
Submission ID: MODEL3896909694
Submission Date: 17 Mar 2008 10:27:13 UTC
Last Modification Date: 27 May 2014 22:24:11 UTC
Creation Date: 16 Mar 2008 19:31:22 UTC
Encoders:  Harish Dharuri
set #1
bqmodel:isDerivedFrom PubMed 9375029
set #2
bqbiol:hasTaxon Taxonomy Eukaryota
bqbiol:isPartOf KEGG Pathway hsa04110
bqbiol:isVersionOf Gene Ontology mitotic cell cycle
Notes

The model reproduces the time profiles of the different species depicted in Fig 3a of the paper. Model successfully 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: 17886749 Submission Date: 17 Mar 2008 10:27:13 UTC Last Modification Date: 27 May 2014 22:24:11 UTC Creation Date: 16 Mar 2008 19:31:22 UTC
Mathematical expressions
Reactions
cycD/CDK4 synthesis cycD/CDK4 degradation cycE/CDK2 synthesis cycE/CDK2 degradation
pRB-p dephosphorilation pRB/E2F complex association pRB/E2F complex deassociation via cycD/CDK4 pRB/E2F complex deassociation via cycE/CDK2
cycle progression cycle break    
Rules
Assignment Rule (variable: E2F) Assignment Rule (variable: RP) Assignment Rule (variable: unpho_RB)  
Physical entities
Compartments Species
cell D E RS
R X E2F
RP    
Global parameters
aD k GF dD
aE af theta dE
pX RT pS pD
qD pE qE aX
f g dX qX
unpho_RB      
Reactions (10)
 
 cycD/CDK4 synthesis  → [D];  
 
 cycD/CDK4 degradation [D] → ;   {D} , {E}
 
 cycE/CDK2 synthesis  → [E];   {E2F}
 
 cycE/CDK2 degradation [E] → ;   {E} , {X}
 
 pRB-p dephosphorilation  → [R];   {RP} , {X}
 
 pRB/E2F complex association [R] → [RS];   {RS} , {R} , {E2F}
 
 pRB/E2F complex deassociation via cycD/CDK4 [RS] → ;   {RS} , {D}
 
 pRB/E2F complex deassociation via cycE/CDK2 [RS] → ;   {RS} , {E}
 
 cycle progression  → [X];   {E} , {E2F} , {X}
 
 cycle break [X] → ;   {X}
 
Rules (3)
 
 Assignment Rule (name: E2F_1) E2F = theta_1-RS_1
 
 Assignment Rule (name: RP_1) RP = RT_1-RS_1-R_1
 
 Assignment Rule (name: unpho_RB) unpho_RB = R_1+RS_1
 
 cell Spatial dimensions: 3.0  Compartment size: 1.0
 
 D
Compartment: cell
Initial amount: 0.1
 
 E
Compartment: cell
Initial amount: 0.6
 
 RS
Compartment: cell
Initial amount: 1.0
 
 R
Compartment: cell
Initial amount: 0.5
 
   X
Compartment: cell
Initial amount: 0.7
 
  E2F
Compartment: cell
 
  RP
Compartment: cell
 
Global Parameters (21)
 
   aD
Value: 0.4
Constant
 
   k
Value: 0.05
Constant
 
   GF
Value: 6.3
Constant
 
   dD
Value: 0.4
Constant
 
   aE
Value: 0.16
Constant
 
   af
Value: 0.9
Constant
 
   theta
Value: 1.5
Constant
 
   dE
Value: 0.2
Constant
 
   pX
Value: 0.48
Constant
 
   RT
Value: 2.5
Constant
 
   pS
Value: 0.6
Constant
 
   pD
Value: 0.48
Constant
 
   qD
Value: 0.6
Constant
 
   pE
Value: 0.096
Constant
 
   qE
Value: 0.6
Constant
 
   aX
Value: 0.08
Constant
 
   f
Value: 0.2
Constant
 
   g
Value: 0.528
Constant
 
   dX
Value: 1.04
Constant
 
   qX
Value: 0.8
Constant
 
   unpho_RB  
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000168

Curator's comment: (updated: 17 Mar 2008 02:51:46 GMT)

The plots correspond to the top and bottom panels of Fig 3a of the paper. Results obtained using MathSBML.

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