Csikasz-Nagy2006 - Mammalian Cell Cycle model
This model originates from the Cell Cycle Database
. It is described in:
Analysis of a generic model of eukaryotic cell-cycle regulation.
Csikász-Nagy A , Battogtokh D , Chen KC , Novák B , Tyson JJ
Biophys. J. [2006 Jun],90(12 ):4361-79
PMID: 16581849
Abstract:
We propose a protein interaction network for the regulation of DNA synthesis and mitosis that emphasizes the universality of the regulatory system among eukaryotic cells. The idiosyncrasies of cell cycle regulation in particular organisms can be attributed, we claim, to specific settings of rate constants in the dynamic network of chemical reactions. The values of these rate constants are determined ultimately by the genetic makeup of an organism. To support these claims, we convert the reaction mechanism into a set of governing kinetic equations and provide parameter values (specific to budding yeast, fission yeast, frog eggs, and mammalian cells) that account for many curious features of cell cycle regulation in these organisms. Using one-parameter bifurcation diagrams, we show how overall cell growth drives progression through the cell cycle, how cell-size homeostasis can be achieved by two different strategies, and how mutations remodel bifurcation diagrams and create unusual cell-division phenotypes. The relation between gene dosage and phenotype can be summarized compactly in two-parameter bifurcation diagrams. Our approach provides a theoretical framework in which to understand both the universality and particularity of cell cycle regulation, and to construct, in modular fashion, increasingly complex models of the networks controlling cell growth and division.
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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.
-
Analysis of a generic model of eukaryotic cell-cycle regulation.
- Csikasz-Nagy A, Battogtokh D, Chen KC, Novák B, Tyson JJ
- Biophysical Journal , 6/ 2006 , Volume 90 , pages: 4361-4379 , PubMed ID: 16581849
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061-0406, USA.
- We propose a protein interaction network for the regulation of DNA synthesis and mitosis that emphasizes the universality of the regulatory system among eukaryotic cells. The idiosyncrasies of cell cycle regulation in particular organisms can be attributed, we claim, to specific settings of rate constants in the dynamic network of chemical reactions. The values of these rate constants are determined ultimately by the genetic makeup of an organism. To support these claims, we convert the reaction mechanism into a set of governing kinetic equations and provide parameter values (specific to budding yeast, fission yeast, frog eggs, and mammalian cells) that account for many curious features of cell cycle regulation in these organisms. Using one-parameter bifurcation diagrams, we show how overall cell growth drives progression through the cell cycle, how cell-size homeostasis can be achieved by two different strategies, and how mutations remodel bifurcation diagrams and create unusual cell-division phenotypes. The relation between gene dosage and phenotype can be summarized compactly in two-parameter bifurcation diagrams. Our approach provides a theoretical framework in which to understand both the universality and particularity of cell cycle regulation, and to construct, in modular fashion, increasingly complex models of the networks controlling cell growth and division.
Submitter of this revision: Krishna Kumar Tiwari
Modellers: Nicolas Le Novère, Krishna Kumar Tiwari
Metadata information
isDescribedBy (1 statement)
hasTaxon (1 statement)
hasProperty (2 statements)
unknownQualifier (1 statement)
isVersionOf (1 statement)
occursIn (1 statement)
Connected external resources
SBGN view in Newt Editor
| Name | Description | Size | Actions |
|---|---|---|---|
Model files |
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| Csikasz-Nagy2006.xml | SBML L2V4 file of the curated model | 377.08 KB | Preview | Download |
Additional files |
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| Csikasz-Nagy2006.cps | COPASI 4.34(build251) file of the curated model | 432.26 KB | Preview | Download |
| Csikasz-Nagy2006.sedml | SEDML file of the curated model | 10.63 KB | Preview | Download |
| MODEL3897771820-biopax2.owl | Auto-generated BioPAX (Level 2) | 38.66 KB | Preview | Download |
| MODEL3897771820-biopax3.owl | Auto-generated BioPAX (Level 3) | 722.00 Bytes | Preview | Download |
| MODEL3897771820.m | Auto-generated Octave file | 22.19 KB | Preview | Download |
| MODEL3897771820.pdf | Auto-generated PDF file | 341.99 KB | Preview | Download |
| MODEL3897771820.png | Auto-generated Reaction graph (PNG) | 326.92 KB | Preview | Download |
| MODEL3897771820.sci | Auto-generated Scilab file | 67.00 Bytes | Preview | Download |
| MODEL3897771820.svg | Auto-generated Reaction graph (SVG) | 79.97 KB | Preview | Download |
| MODEL3897771820.vcml | Auto-generated VCML file | 88.31 KB | Preview | Download |
| MODEL3897771820.xpp | Auto-generated XPP file | 17.67 KB | Preview | Download |
| MODEL3897771820_url.xml | SBML L2V1 representation of Csikasz-Nagy2006_Cell_Cycle - author submitted | 66.57 KB | Preview | Download |
| MODEL3897771820_urn.xml | Auto-generated SBML file with URNs | 75.20 KB | Preview | Download |
- Model originally submitted by : Nicolas Le Novère
- Submitted: Nov 28, 2008 3:34:39 PM
- Last Modified: Nov 22, 2021 4:36:22 PM
Revisions
-
Version: 4
- Submitted on: Nov 22, 2021 4:36:22 PM
- Submitted by: Krishna Kumar Tiwari
- With comment: Automatically added model identifier BIOMD0000001044
-
Version: 2
- Submitted on: Jul 20, 2012 12:39:44 PM
- Submitted by: Nicolas Le Novère
- With comment: Current version of Csikasz-Nagy2006_Cell_Cycle
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Version: 1
- Submitted on: Nov 28, 2008 3:34:39 PM
- Submitted by: Nicolas Le Novère
- With comment: Original import of New Mechanism
(*) You might be seeing discontinuous
revisions as only public revisions are displayed here. Any private revisions
of this model will only be shown to the submitter and their collaborators.
: Variable used inside SBML models
| Species | Initial Concentration/Amount |
|---|---|
| CKIT | 0.295407682657242 item |
| CycBT | 0.166841372847557 item |
| CycAT | 0.00994044542312622 item |
| APC | [] |
| Cdc20i | 0.018553527072072 item |
| Cdh1i | 0.99923574924469 item |
| CKI | 0.295407682657242 item |
| preMPF | 0.0 item |
| BCKI | 0.0 item |
| Reactions | Rate | Parameters |
|---|---|---|
| CKIT = CKI+BCKI+pBCKI+TriA+TriE | [] | [] |
| CycBT = CycB+pB+BCKI+pBCKI | [] | [] |
| CycAT = CycA+TriA | [] | [] |
| APC => APCP; CycB | kaie*APC*CycB/(Jaie+APC) | kaie = 0.07; Jaie = 0.01 |
| => Cdc20i; CycB | ks20a+ks20b*CycB^n20/(J20^n20+CycB^n20) | ks20a = 0.0; J20 = 1.0; ks20b = 0.15; n20 = 1.0 |
| Cdh1 => Cdh1i | 1*Cdh1*Vih1/(Jih1+Cdh1) | Jih1 = 0.01; Vih1 = NaN |
| CycB + CKI => BCKI | kassb*CycB*CKI | kassb = 0.0 |
| preMPF = pB+pBCKI | [] | [] |
| TriE => CKI | Vde*TriE | Vde = NaN |
(added: 22 Nov 2021, 16:35:58, updated: 22 Nov 2021, 16:35:58)