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BIOMD0000000167 - Mayya2005_STATmodule

 

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Reference Publication
Publication ID: 17091582
Mayya V, Loew LM.
STAT module can function as a biphasic amplitude filter.
Syst Biol (Stevenage) 2005 Mar; 2(1): 43-52
Department of Cell Biology and Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington 06030, USA. les@volt.uchc.edu  [more]
Model
Original Model: VCell logo
Submitter: Harish Dharuri
Submission ID: MODEL6095659304
Submission Date: 25 Feb 2008 00:07:51 UTC
Last Modification Date: 27 May 2014 22:17:03 UTC
Creation Date: 26 Sep 2007 02:22:36 UTC
Encoders:  Harish Dharuri
set #1
bqmodel:isDerivedFrom BioModels Database Yamada2003_JAK_STAT_SOCS1_knockout
BioModels Database Yamada2003_JAK_STAT_pathway
PubMed 15240442
PubMed 12552139
set #2
bqbiol:isVersionOf Gene Ontology regulation of tyrosine phosphorylation of STAT protein
bqbiol:hasPart KEGG Pathway Jak-STAT signaling pathway - Homo sapiens (human)
bqbiol:hasTaxon Taxonomy cellular organisms
Notes

The model reproduces Fig 2B 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: 17091582 Submission Date: 25 Feb 2008 00:07:51 UTC Last Modification Date: 27 May 2014 22:17:03 UTC Creation Date: 26 Sep 2007 02:22:36 UTC
Mathematical expressions
Reactions
PstatDimerisation statDephosphorylation statPhosphorylation PstatDimerisationNuc
PstatDimer_ import stat_export stat_import  
Rules
Assignment Rule (variable: statKinase_sol)      
Physical entities
Compartments Species
nuc PstatDimer_nuc stat_nuc Pstat_nuc
statPhosphatase_nuc    
sol stat_sol Pstat_sol statKinase_sol
PstatDimer_sol species_test  
nm      
Reactions (7)
 
 PstatDimerisation 2.0 × [Pstat_sol] ↔ [PstatDimer_sol];  
 
 statDephosphorylation [Pstat_nuc] ↔ [stat_nuc];   {statPhosphatase_nuc}
 
 statPhosphorylation [stat_sol] ↔ [Pstat_sol] + [species_test];   {statKinase_sol}
 
 PstatDimerisationNuc 2.0 × [Pstat_nuc] ↔ [PstatDimer_nuc];  
 
 PstatDimer_ import [PstatDimer_sol] ↔ [PstatDimer_nuc];  
 
 stat_export [stat_sol] ↔ [stat_nuc];  
 
 stat_import [stat_sol] ↔ [stat_nuc];  
 
Rules (1)
 
 Assignment Rule (name: statKinase_sol) statKinase_sol = piecewise(0.01*sin(0.001571*(-500+t)), ((t > 500)) && ((t < 2502.54614894971)), 0)
 
 nuc Spatial dimensions: 3.0  Compartment size: 1.0  (Units: litre)
 
 PstatDimer_nuc
Compartment: nuc
Initial concentration: 0.0
 
 stat_nuc
Compartment: nuc
Initial concentration: 0.0
 
 Pstat_nuc
Compartment: nuc
Initial concentration: 0.0
 
 statPhosphatase_nuc
Compartment: nuc
Initial concentration: 0.05
 
 sol Spatial dimensions: 3.0  Compartment size: 14.625  (Units: litre)
 
 stat_sol
Compartment: sol
Initial concentration: 1.0
 
 Pstat_sol
Compartment: sol
Initial concentration: 0.0
 
  statKinase_sol
Compartment: sol
 
 PstatDimer_sol
Compartment: sol
Initial concentration: 0.0
 
   species_test
Compartment: sol
Initial concentration: 0.0
 
 nm Spatial dimensions: 2.0  Compartment size: 1.0  (Units: um2)
PstatDimerisation (2)
 
   Kf_PstatDimerisation
Value: 0.6   (Units: uM_1_s_1)
Constant
 
   Kr_PstatDimerisation
Value: 0.03   (Units: s_1)
Constant
 
statDephosphorylation (2)
 
   Kcat_dephos
Value: 1.0   (Units: s_1)
Constant
 
   Km_dephos
Value: 2.0   (Units: uM)
Constant
 
statPhosphorylation (2)
 
   Kcat_phos
Value: 1.0   (Units: s_1)
Constant
 
   Km_phos
Value: 4.0   (Units: uM)
Constant
 
PstatDimerisationNuc (2)
 
   Kf_PstatDimerisation
Value: 0.6   (Units: uM_1_s_1)
Constant
 
   Kr_PstatDimerisation
Value: 0.03   (Units: s_1)
Constant
 
PstatDimer_ import (2)
 
   PstatDimer_impMax
Value: 0.045   (Units: uM_um_s_1)
Constant
 
   Kpsd_imp
Value: 0.3   (Units: uM)
Constant
 
stat_export (2)
 
   stat_expMax
Value: -0.06   (Units: uM_um_s_1)
Constant
 
   Ks_exp
Value: 0.6   (Units: uM)
Constant
 
stat_import (2)
 
   stat_impMax
Value: 0.003   (Units: uM_um_s_1)
Constant
 
   Ks_imp
Value: 3.0   (Units: uM)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000167

Curator's comment: (updated: 31 Jan 2008 17:52:19 GMT)

Plots correspond to Fig 2 of the paper. Results obtained using MathSBML.

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