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BIOMD0000000125 - Komarova2005_TheoreticalFramework_BasicArchitecture

 

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Reference Publication
Publication ID: 16729058
Komarova NL, Zou X, Nie Q, Bardwell L.
A theoretical framework for specificity in cell signaling.
Mol. Syst. Biol. 2005; 1: 2005.0023
Department of Mathematics, University of California, Irvine, CA 92697, USA. komarova@uci.edu  [more]
Model
Original Model: BIOMD0000000125.origin
Submitter: Enuo He
Submission ID: MODEL2451230486
Submission Date: 05 Jul 2007 08:23:34 UTC
Last Modification Date: 05 Jul 2012 16:31:20 UTC
Creation Date: 04 Jun 2007 15:33:08 UTC
Encoders:  Enuo He
set #1
bqbiol:occursIn Taxonomy Opisthokonta
bqbiol:hasVersion KEGG Pathway MAPK signaling pathway
Gene Ontology MAPK cascade
bqbiol:isVersionOf Gene Ontology cell surface receptor signaling pathway
Gene Ontology cellular response to stimulus
Gene Ontology receptor signaling complex scaffold activity
Notes

This model according to the paper A Theoretical Framework for Specificity in Cell Signalling The model is "basic architecture" of Figure2A. Figure2B, Figure2C have been reproduced by MathSBML. The reproduced figures are slightly different from the original ones in the paper, the peak of [x2] is higher than 1 and is not decreasing dramatically when [x0]=0. And I think maybe the author shift the or scale the curves.


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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.

Model
Publication ID: 16729058 Submission Date: 05 Jul 2007 08:23:34 UTC Last Modification Date: 05 Jul 2012 16:31:20 UTC Creation Date: 04 Jun 2007 15:33:08 UTC
Mathematical expressions
Reactions
x0 activates x1 y0 activates x1 x1 activates x2 x1 activates y2
x1 deactivation x2 deactivation y2 deactivation  
Events
event_0000001      
Physical entities
Compartments Species
cell x1 x2 y2
x0 y0  
Global parameters
a1 a2 b1 b2
d1 d2x d2y  
Reactions (7)
 
 x0 activates x1  → [x1];   {x0}
 
 y0 activates x1  → [x1];   {y0}
 
 x1 activates x2  → [x2];   {x1}
 
 x1 activates y2  → [y2];   {x1}
 
 x1 deactivation [x1] → ;  
 
 x2 deactivation [x2] → ;  
 
 y2 deactivation [y2] → ;  
 
Events (1)
 
 event_0000001
x0 = 0
 
 cell Spatial dimensions: 3.0  Compartment size: 1.0
 
 x1
Compartment: cell
Initial concentration: 0.0
 
   x2
Compartment: cell
Initial concentration: 0.0
 
   y2
Compartment: cell
Initial concentration: 0.0
 
 x0
Compartment: cell
Initial concentration: 1.0
 
 y0
Compartment: cell
Initial concentration: 0.0
 
Global Parameters (7)
 
   a1
Value: 2.0
Constant
 
   a2
Value: 2.0
Constant
 
   b1
Value: 1.0
Constant
 
   b2
Value: 1.0
Constant
 
   d1
Value: 1.0
Constant
 
   d2x
Value: 1.0
Constant
 
   d2y
Value: 1.0
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000125

Curator's comment: (updated: 21 Jun 2007 19:42:37 BST)

Figure2B left figure reproduced by MathSBML.

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