public model
Short description

The model reproduces Fig 6B of the paper for model 6. The model was reproduced using XPP.

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.

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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.

Related Publication
  • Oscillations and variability in the p53 system.
  • Geva-Zatorsky N, Rosenfeld N, Itzkovitz S, Milo R, Sigal A, Dekel E, Yarnitzky T, Liron Y, Polak P, Lahav G, Alon U
  • Molecular Systems Biology , 0/ 2006 , Volume 2 , pages: 2006.0033
  • Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
  • Understanding the dynamics and variability of protein circuitry requires accurate measurements in living cells as well as theoretical models. To address this, we employed one of the best-studied protein circuits in human cells, the negative feedback loop between the tumor suppressor p53 and the oncogene Mdm2. We measured the dynamics of fluorescently tagged p53 and Mdm2 over several days in individual living cells. We found that isogenic cells in the same environment behaved in highly variable ways following DNA-damaging gamma irradiation: some cells showed undamped oscillations for at least 3 days (more than 10 peaks). The amplitude of the oscillations was much more variable than the period. Sister cells continued to oscillate in a correlated way after cell division, but lost correlation after about 11 h on average. Other cells showed low-frequency fluctuations that did not resemble oscillations. We also analyzed different families of mathematical models of the system, including a novel checkpoint mechanism. The models point to the possible source of the variability in the oscillations: low-frequency noise in protein production rates, rather than noise in other parameters such as degradation rates. This study provides a view of the extensive variability of the behavior of a protein circuit in living human cells, both from cell to cell and in the same cell over time.
Harish Dharuri

Metadata information

BioModels Database MODEL0076407823
BioModels Database BIOMD0000000155
BioModels Database BIOMD0000000156
BioModels Database BIOMD0000000154
BioModels Database BIOMD0000000159
BioModels Database BIOMD0000000158
BioModels Database BIOMD0000000157
PubMed 16773083
Taxonomy Homo sapiens
Mathematical Modelling Ontology Ordinary differential equation model
Brenda Tissue Ontology MCF-7 cell

Curation status

Name Description Size Actions

Model files

BIOMD0000000155_url.xml SBML L2V1 representation of Zatorsky2006_p53_Model6 12.57 KB Preview | Download

Additional files

BIOMD0000000155_urn.xml Auto-generated SBML file with URNs 13.92 KB Preview | Download
BIOMD0000000155.m Auto-generated Octave file 4.03 KB Preview | Download
BIOMD0000000155-biopax3.owl Auto-generated BioPAX (Level 3) 11.94 KB Preview | Download
BIOMD0000000155-biopax2.owl Auto-generated BioPAX (Level 2) 10.01 KB Preview | Download
BIOMD0000000155.sci Auto-generated Scilab file 163.00 bytes Preview | Download
BIOMD0000000155.vcml Auto-generated VCML file 900.00 bytes Preview | Download
BIOMD0000000155.pdf Auto-generated PDF file 142.70 KB Preview | Download
BIOMD0000000155.png Auto-generated Reaction graph (PNG) 11.02 KB Preview | Download
BIOMD0000000155.xpp Auto-generated XPP file 2.19 KB Preview | Download
BIOMD0000000155.svg Auto-generated Reaction graph (SVG) 8.22 KB Preview | Download

  • Model originally submitted by : Harish Dharuri
  • Submitted: Jan 14, 2008 9:30:52 PM
  • Last Modified: Mar 20, 2014 4:35:42 PM
  • Version: 2 public model Download this version
    • Submitted on: Mar 20, 2014 4:35:42 PM
    • Submitted by: Harish Dharuri
    • With comment: Current version of Zatorsky2006_p53_Model6
  • Version: 1 public model Download this version
    • Submitted on: Jan 14, 2008 9:30:52 PM
    • Submitted by: Harish Dharuri
    • With comment: Original import of Zatorsky2006_p53_Model6
Curator's comment:
(added: 11 Jan 2008, 22:27:53, updated: 11 Jan 2008, 22:27:53)
Plot corresponds to Fig 6B for model 6. Simulation result obtained using xpp.