Haberichter2007_cellcycle

  public model
Model Identifier
BIOMD0000000109
Short description

This model is according to the paper A systems biology dynamical model of mammalian G1 cell cycle progression. Supplementary Figure 2A has been reproduced by the MathSBML and CellDesigner. All the data of this model are from the set 2 of Supplementary talbe2.


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.

Format
SBML (L2V1)
Related Publication
  • A systems biology dynamical model of mammalian G1 cell cycle progression.
  • Haberichter T, Mädge B, Christopher RA, Yoshioka N, Dhiman A, Miller R, Gendelman R, Aksenov SV, Khalil IG, Dowdy SF
  • Molecular Systems Biology , 0/ 2007 , Volume 3 , pages: 84 , PubMed ID: 17299420
  • Gene Network Sciences Inc., Cambridge, MA 02141, USA.
  • The current dogma of G(1) cell-cycle progression relies on growth factor-induced increase of cyclin D:Cdk4/6 complex activity to partially inactivate pRb by phosphorylation and to sequester p27(Kip1)-triggering activation of cyclin E:Cdk2 complexes that further inactivate pRb. pRb oscillates between an active, hypophosphorylated form associated with E2F transcription factors in early G(1) phase and an inactive, hyperphosphorylated form in late G(1), S and G(2)/M phases. However, under constant growth factor stimulation, cells show constitutively active cyclin D:Cdk4/6 throughout the cell cycle and thereby exclude cyclin D:Cdk4/6 inactivation of pRb. To address this paradox, we developed a mathematical model of G(1) progression using physiological expression and activity profiles from synchronized cells exposed to constant growth factors and included a metabolically responsive, activating modifier of cyclin E:Cdk2. Our mathematical model accurately simulates G(1) progression, recapitulates observations from targeted gene deletion studies and serves as a foundation for development of therapeutics targeting G(1) cell-cycle progression.
Contributors
Enuo He

Metadata information

is
BioModels Database MODEL3734058719
BioModels Database BIOMD0000000109
isDescribedBy
PubMed 17299420
hasTaxon
Taxonomy Mammalia
isVersionOf
Gene Ontology G1 phase
hasVersion

Curation status
Curated

Tags
Name Description Size Actions

Model files

BIOMD0000000109_url.xml SBML L2V1 representation of Haberichter2007_cellcycle 205.56 KB Preview | Download

Additional files

BIOMD0000000109.xpp Auto-generated XPP file 27.78 KB Preview | Download
BIOMD0000000109.sci Auto-generated Scilab file 67.00 Bytes Preview | Download
BIOMD0000000109.m Auto-generated Octave file 37.05 KB Preview | Download
BIOMD0000000109.png Auto-generated Reaction graph (PNG) 3.31 MB Preview | Download
BIOMD0000000109.vcml Auto-generated VCML file 296.77 KB Preview | Download
BIOMD0000000109_urn.xml Auto-generated SBML file with URNs 218.29 KB Preview | Download
BIOMD0000000109-biopax3.owl Auto-generated BioPAX (Level 3) 338.13 KB Preview | Download
BIOMD0000000109.svg Auto-generated Reaction graph (SVG) 314.69 KB Preview | Download
BIOMD0000000109-biopax2.owl Auto-generated BioPAX (Level 2) 190.28 KB Preview | Download
BIOMD0000000109.pdf Auto-generated PDF file 651.85 KB Preview | Download

  • Model originally submitted by : Enuo He
  • Submitted: 17-Apr-2007 22:11:32
  • Last Modified: 05-Jul-2012 15:49:20
Revisions
  • Version: 2 public model Download this version
    • Submitted on: 05-Jul-2012 15:49:20
    • Submitted by: Enuo He
    • With comment: Current version of Haberichter2007_cellcycle
  • Version: 1 public model Download this version
    • Submitted on: 17-Apr-2007 22:11:32
    • Submitted by: Enuo He
    • With comment: Original import of BIOMD0000000109.xml.origin

(*) You might be seeing discontinuous revisions as only public revisions are displayed here. Any private revisions unpublished model revision of this model will only be shown to the submitter and their collaborators.

Legends
: Variable used inside SBML models


Species
Reactions
Reactions Rate Parameters
APCCYEmi1 => APCC kdYEmi1*APCCYEmi1*X kdYEmi1 = 0.018158
CyclinA + APCC => APCCYCyclinAYInt X*kbYAPCCYYCyclinA*CyclinA*APCC kbYAPCCYYCyclinA = 1.61E-5
APCCYCyclinAYInt => CyclinA + APCC X*kuYAPCCYYCyclinA*APCCYCyclinAYInt kuYAPCCYYCyclinA = 0.1
Cdk2Y002 + APCC => APCCYCdk2Y000YCdk2Y002YInt X*kbYAPCCYYCyclinA*Cdk2Y002*APCC kbYAPCCYYCyclinA = 1.61E-5
APCCYCdk2Y000YCdk2Y002YInt => Cdk2Y002 + APCC X*kuYAPCCYYCyclinA*APCCYCdk2Y000YCdk2Y002YInt kuYAPCCYYCyclinA = 0.1
APCCYCdk2Y000YCdk2Y002YInt => Cdk2Y000 + APCC X*kudYAPCCYYCyclinA*APCCYCdk2Y000YCdk2Y002YInt kudYAPCCYYCyclinA = 4.999555
Cdk2Y102 + APCC => APCCYCdk2Y100YCdk2Y102YInt X*kbYAPCCYYCyclinA*Cdk2Y102*APCC kbYAPCCYYCyclinA = 1.61E-5
APCCYCdk2Y100YCdk2Y102YInt => Cdk2Y102 + APCC X*kuYAPCCYYCyclinA*APCCYCdk2Y100YCdk2Y102YInt kuYAPCCYYCyclinA = 0.1
Cdk2Y012 + APCC => APCCYCdk2Y010YCdk2Y012YInt; Cdk2Y102 X*kbYAPCCYYCyclinA*Cdk2Y102*APCC kbYAPCCYYCyclinA = 1.61E-5
APCCYCdk2Y010YCdk2Y012YInt => Cdk2Y010 + APCC X*kudYAPCCYYCyclinA*APCCYCdk2Y010YCdk2Y012YInt kudYAPCCYYCyclinA = 4.999555
APCCYCdk2Y110YCdk2Y112YInt => Cdk2Y112 + APCC X*kuYAPCCYYCyclinA*APCCYCdk2Y110YCdk2Y112YInt kuYAPCCYYCyclinA = 0.1
Cdk1Y01 + APCC => APCCYCdk1Y00YCdk1Y01YInt X*kbYAPCCYYCyclinA*Cdk1Y01*APCC kbYAPCCYYCyclinA = 1.61E-5
Cdk2Y011YpRbY10YpRbY20YInt => pRbY10 + Cdk2Y011 X*kuYE2YYpRb*Cdk2Y011YpRbY10YpRbY20YInt kuYE2YYpRb = 0.1
Cdk2Y011YpRbY10YpRbY20YInt => pRbY20 + Cdk2Y011 X*kupYE2YYpRb*Cdk2Y011YpRbY10YpRbY20YInt kupYE2YYpRb = 4.78271
Cdk2Y011YpRbY11YpRbY21YInt => pRbY11 + Cdk2Y011 X*kuYE2YYpRb*Cdk2Y011YpRbY11YpRbY21YInt kuYE2YYpRb = 0.1
Curator's comment:
(added: 17 Apr 2007, 21:40:08, updated: 17 Apr 2007, 21:40:08)
Supplementary Figure2A has been reproduced by the MathSBML and CellDesigner.