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BIOMD0000000499 - Vizan2013 - TGF pathway long term signaling

 

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Reference Publication
Publication ID: 24327760
Vizán P, Miller DS, Gori I, Das D, Schmierer B, Hill CS.
Controlling long-term signaling: receptor dynamics determine attenuation and refractory behavior of the TGF-β pathway.
Sci Signal 2013 Dec; 6(305): ra106
1Developmental Signalling Laboratory, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK.  [more]
Model
Original Model: BIOMD0000000499.origin
Submitter: Bernhard Schmierer
Submission ID: MODEL1203120000
Submission Date: 12 Mar 2012 16:12:51 UTC
Last Modification Date: 24 Feb 2014 09:47:15 UTC
Creation Date: 16 Dec 2013 11:13:07 UTC
Encoders:  Nick Juty
   Pedro Vizán
set #1
bqmodel:isDerivedFrom BioModels Database Schmierer_2008_Smad_Tgfb
set #2
bqbiol:isVersionOf Gene Ontology SMAD protein signal transduction
Gene Ontology transforming growth factor beta receptor signaling pathway
bqmodel:is BioModels Database MODEL1203120000
bqbiol:hasTaxon Taxonomy Homo sapiens
set #3
bqmodel:is BioModels Database BIOMD0000000499
Notes
Model
Publication ID: 24327760 Submission Date: 12 Mar 2012 16:12:51 UTC Last Modification Date: 24 Feb 2014 09:47:15 UTC Creation Date: 16 Dec 2013 11:13:07 UTC
Mathematical expressions
Rules
Assignment Rule (variable: S24n) Assignment Rule (variable: S4fc) Assignment Rule (variable: KDiss) Assignment Rule (variable: kon)
Assignment Rule (variable: kex4) Assignment Rule (variable: Ktr) Assignment Rule (variable: pS2fc) Assignment Rule (variable: Rtot)
Assignment Rule (variable: Rcom_I) Assignment Rule (variable: Rcom_S) Assignment Rule (variable: S2n) Assignment Rule (variable: S22n)
Assignment Rule (variable: S4n) Assignment Rule (variable: S4fn) Assignment Rule (variable: pS2n) Assignment Rule (variable: pS2fn)
Assignment Rule (variable: Total Nuc S2 for fit) Rate Rule (variable: S22) Rate Rule (variable: S24) Rate Rule (variable: pS2tot)
Rate Rule (variable: TGF) Rate Rule (variable: R) Rate Rule (variable: S2c) Rate Rule (variable: Rcom)
Rate Rule (variable: pS2c) Rate Rule (variable: S22c) Rate Rule (variable: S24c) Rate Rule (variable: S4c)
Rate Rule (variable: RT) Rate Rule (variable: Ract)    
Physical entities
Compartments Species
Cell S22 S24 pS2tot
TGF R S2c
Rcom pS2c Rcom_S
S2n S22n S4n
S22c pS2n pS2fn
S24n S24c S4fc
S4c pS2fc S4fn
SBI Rtot RT
Rcom_I Ract  
Global parameters
kd kex kin alpha
CHX kp kdp koff
kon KDiss CIF D
a S2tot S4tot rc0
KSBI k'T kex4 Total Nuc S2 for fit
Ktr k'act Tmax in ng/ml TSca
k'cc k'synT k'synTbas MG132
Initial for S2n      
Reactions (0)
Rules (30)
 
 Assignment Rule (name: species_16) S24n = (parameter_13+1)*species_2-parameter_13*species_17
 
 Assignment Rule (name: species_18) S4fc = species_19-species_17
 
 Assignment Rule (name: parameter_10) KDiss = 0.171
 
 Assignment Rule (name: parameter_9) kon = parameter_8/parameter_10
 
 Assignment Rule (name: parameter_19) kex4 = parameter_3
 
 Assignment Rule (name: parameter_21) Ktr = parameter_16/(1-parameter_16)*(parameter_4+1)/parameter_4
 
 Assignment Rule (name: species_20) pS2fc = (species_8-2*species_13)-species_17
 
 Assignment Rule (name: species_23) Rtot = species_5+species_7+species_24+species_26
 
 Assignment Rule (name: species_25) Rcom_I = species_7*1/(1+parameter_21)
 
 Assignment Rule (name: species_9) Rcom_S = species_7*parameter_21/(1+parameter_21)
 
 Assignment Rule (name: species_10) S2n = (parameter_13+1)*(parameter_14-species_3)-parameter_13*species_6
 
 Assignment Rule (name: species_11) S22n = (parameter_13+1)*species_1-parameter_13*species_13
 
 Assignment Rule (name: species_12) S4n = (parameter_13+1)*parameter_15-parameter_13*species_19
 
 Assignment Rule (name: species_21) S4fn = species_12-species_16
 
 Assignment Rule (name: species_14) pS2n = (parameter_13+1)*species_3-parameter_13*species_8
 
 Assignment Rule (name: species_15) pS2fn = (species_14-2*species_11)-species_16
 
 Assignment Rule (name: parameter_20) Total Nuc S2 for fit = (species_10+species_14)/Metabolite_9
 
 Rate Rule (name: species_1) d [ S22] / d t= 1/(1+parameter_13)*(parameter_9*(parameter_13*species_20^2+species_15^2)-parameter_8*(parameter_13*species_13+species_11))
 
 Rate Rule (name: species_2) d [ S24] / d t= 1/(parameter_13+1)*(parameter_9*(parameter_13*species_18*species_20+species_15*species_21)-parameter_8*(parameter_13*species_17+species_16))
 
 Rate Rule (name: species_3) d [ pS2tot] / d t= 1/(1+parameter_13)*(parameter_13*parameter_6*species_26*parameter_17/(parameter_17+species_22)*species_6-parameter_7*species_15)
 
 Rate Rule (name: species_4) d [ TGF] / d t= parameter_1*((parameter_27+parameter_26*species_16)-(parameter_18*species_9+parameter_25)*species_4)
 
 Rate Rule (name: species_5) d [ R] / d t= parameter_1*((1-parameter_5)*(1-parameter_16)-(parameter_4+(1-parameter_28))*species_5)
 
 Rate Rule (name: species_6) d [ S2c] / d t= parameter_2*species_10-(parameter_3+parameter_6*species_26*parameter_17/(parameter_17+species_22))*species_6
 
 Rate Rule (name: species_7) d [ Rcom] / d t= parameter_1*((parameter_4*species_5-(1-parameter_28)*species_25)-parameter_18*species_4*species_9)
 
 Rate Rule (name: species_8) d [ pS2c] / d t= (parameter_6*species_26*parameter_17/(parameter_17+species_22)*species_6+parameter_2*species_15)-parameter_3*(species_20+parameter_11*(species_17+2*species_13))
 
 Rate Rule (name: species_13) d [ S22c] / d t= parameter_9*species_20^2-(parameter_8+parameter_3*parameter_11)*species_13
 
 Rate Rule (name: species_17) d [ S24c] / d t= parameter_9*species_18*species_20-(parameter_8+parameter_3*parameter_11)*species_17
 
 Rate Rule (name: species_19) d [ S4c] / d t= parameter_19*species_21-parameter_3*(species_18+parameter_11*species_17)
 
 Rate Rule (name: species_24) d [ RT] / d t= parameter_1*(parameter_18*species_4*species_9-(parameter_22+parameter_12*(1-parameter_28))*species_24)
 
 Rate Rule (name: species_26) d [ Ract] / d t= parameter_1*(parameter_22*species_24-parameter_12*(1-parameter_28)*species_26)
 
 Cell Spatial dimensions: 3.0  Compartment size: 1.0
 
 S22
Compartment: Cell
Initial concentration: 0.0
 
 S24
Compartment: Cell
Initial concentration: 0.0
 
 pS2tot
Compartment: Cell
Initial concentration: 0.0
 
 TGF
Compartment: Cell
Initial concentration: 4.0
 
 R
Compartment: Cell
Initial concentration: 0.87962962962963
 
 S2c
Compartment: Cell
Initial concentration: 1.19430241051863
 
 Rcom
Compartment: Cell
Initial concentration: 0.12037037037037
 
 pS2c
Compartment: Cell
Initial concentration: 0.0
 
  Rcom_S
Compartment: Cell
Initial concentration: 0.05
 
  S2n
Compartment: Cell
Initial concentration: 0.558933528122717
 
  S22n
Compartment: Cell
Initial concentration: 0.0
 
  S4n
Compartment: Cell
Initial concentration: 1.0
 
 S22c
Compartment: Cell
Initial concentration: 0.0
 
  pS2n
Compartment: Cell
Initial concentration: 0.0
 
  pS2fn
Compartment: Cell
Initial concentration: 0.0
 
  S24n
Compartment: Cell
Initial concentration: 0.0
 
 S24c
Compartment: Cell
Initial concentration: 0.0
 
  S4fc
Compartment: Cell
Initial concentration: 1.0
 
 S4c
Compartment: Cell
Initial concentration: 1.0
 
  pS2fc
Compartment: Cell
Initial concentration: 0.0
 
  S4fn
Compartment: Cell
Initial concentration: 1.0
 
 SBI
Compartment: Cell
Initial concentration: 0.0
 
  Rtot
Compartment: Cell
Initial concentration: 1.0
 
 RT
Compartment: Cell
Initial concentration: 0.0
 
  Rcom_I
Compartment: Cell
Initial concentration: 0.0703703703703704
 
 Ract
Compartment: Cell
Initial concentration: 0.0
 
Global Parameters (29)
 
 kd
Value: 0.32
Constant
 
 kex
Value: 20.0
Constant
 
 kin
Value: 9.36
Constant
 
 alpha
Value: 0.08
Constant
 
 CHX
Constant
 
 kp
Value: 21.3715
Constant
 
 kdp
Value: 24.0
Constant
 
 koff
Value: 60.0
Constant
 
  kon
Value: 350.877192982456
 
  KDiss
Value: 0.171
 
 CIF
Value: 5.7
Constant
 
 D
Value: 4.0
Constant
 
 a
Value: 2.27
Constant
 
 S2tot
Value: 1.0
Constant
 
 S4tot
Value: 1.0
Constant
 
 rc0
Value: 0.05
Constant
 
 KSBI
Value: 0.196565
Constant
 
 k'T
Value: 100.0
Constant
 
  kex4
Value: 9.36
 
  Total Nuc S2 for fit
Value: 1.0
 
  Ktr
Value: 0.710526315789474
 
 k'act
Value: 24.5383
Constant
 
 Tmax in ng/ml
Value: 2.0
Constant
 
 TSca
Value: 2.0
Constant
 
 k'cc
Value: 0.35
Constant
 
 k'synT
Constant
 
 k'synTbas
Constant
 
 MG132
Constant
 
 Initial for S2n
Value: 0.558933528122717
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000499

Curator's comment: (updated: 15 Jan 2014 11:32:18 GMT)

The curation figure reproduces the results shown in Figure 4B of the reference publication, and was generated using SBMLsimulator 1.1.The names given to the physical entity names in the model do not correspond with those in the reference publication. The curation figure provides the latter in parentheses.

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