BIOMD0000000288
type: SBMLModel
parameter: 335502
curated: true
species: 335362
species: 335382
rule: 335424
species: 335361
rule: 335425
occurs in: http://identifiers.org/taxonomy/9606
rule: 335421
rule: 335420
parameter: 335443
parameter: 335453
species: 335377
parameter: 335459
parameter: 335469
time units: 044889
parameter: 335488
parameter: 335492
species: 335376
species: 335371
parameter: 335474
reaction: 335403
species: 335366
parameter: 335499
species: 335386
reaction: 335398
species: 335365
species: 335385
parameter: 335433
parameter: 335439
parameter: 335449
reaction: 335400
species: 335381
parameter: 335467
parameter: 335477
parameter: 335503
reaction: 335404
reaction: 335395
length unit: 879216
parameter: 335454
parameter: 335464
species: 335360
parameter: 335489
is version of: GO:0070371
species: 335370
parameter: 335493
species: 335359
parameter: 335431
species: 335375
parameter: 335447
parameter: 335457
is version of: GO:0048008
is version of: GO:0014065
reaction: 335393
parameter: 335434
parameter: 335444
parameter: 335462
parameter: 335472
is part of: ko04010
reaction: 335390
parameter: 335478
reaction: 335405
parameter: 335482
parameter: 335487
parameter: 335497
reaction: 335388
species: 335380
rule: 335429
area units: metaid_0000005
notes: This model is from the article: PI3K-dependent cross-talk interactions converge with Ras as quantifiable inputs integrated by Erk. Wang CC, Cirit M, Haugh JM Mol. Syst. Biol. 2009;5:246. 19225459 , Abstract: Although it is appreciated that canonical signal-transduction pathways represent dominant modes of regulation embedded in larger interaction networks, relatively little has been done to quantify pathway cross-talk in such networks. Through quantitative measurements that systematically canvas an array of stimulation and molecular perturbation conditions, together with computational modeling and analysis, we have elucidated cross-talk mechanisms in the platelet-derived growth factor (PDGF) receptor signaling network, in which phosphoinositide 3-kinase (PI3K) and Ras/extracellular signal-regulated kinase (Erk) pathways are prominently activated. We show that, while PI3K signaling is insulated from cross-talk, PI3K enhances Erk activation at points both upstream and downstream of Ras. The magnitudes of these effects depend strongly on the stimulation conditions, subject to saturation effects in the respective pathways and negative feedback loops. Motivated by those dynamics, a kinetic model of the network was formulated and used to precisely quantify the relative contributions of PI3K-dependent and -independent modes of Ras/Erk activation. This model is parameterized with the median of the estimated parameters given in the supplementary material of the original publication's (doi: 10.1038/msb.2009.4 ) supplement on pages 8 and 9. This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2010 The BioModels.net Team. 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 en…
parameter: 335437
reaction: 335399
parameter: 335484
reaction: 335408
volume units: 982936
parameter: 335494
is described by: http://identifiers.org/pubmed/19225459
is part of: ko04012
rule: 335426

335502
type: Parameter
is: SBO:0000190
constant: true
value: 1.98

335362
type: Species
is version of: Q15198
is: SBO:0000420
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 335358

335358
type: Compartment
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is: SBO:0000290
constant: true
size: 1.0
spatial dimensions: 3.0

335382
type: Species
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is: SBO:0000245
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 335358

335361
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boundary condition: false
initial concentration: NaN
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has only substance units: false
has part: Q9NRA1
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initial amount: NaN
in compartment: 335358
is: SBO:0000296

335443
type: Parameter
is: SBO:0000002
constant: true
value: 1.0

335453
type: Parameter
is: SBO:0000009
constant: true
value: 2.85

335377
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is: SBO:0000245
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 335358

335459
type: Parameter
is: SBO:0000002
constant: true
value: 0.405

335469
type: Parameter
is: SBO:0000002
constant: true
value: 1.09

335488
type: Parameter
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constant: true
value: 31.5

335492
type: Parameter
is: SBO:0000002
constant: true
value: 0.272

335376
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constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 335358

335371
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is: SBO:0000014
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 335358

335474
type: Parameter
is: SBO:0000027
constant: true
value: 7.99

335403
type: Reaction
fast: false
reversible: true

335380
type: Species
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is: SBO:0000245
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.0
initial amount: NaN
in compartment: 335358

335387
type: Species
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is: SBO:0000245
constant: false
boundary condition: false
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initial concentration: 1.0
initial amount: NaN
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335381
type: Species
is version of: P27361
is: SBO:0000245
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 335358

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type: SpeciesReference
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335366
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is: SBO:0000236
constant: false
boundary condition: false
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initial concentration: 0.0
initial amount: NaN
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335499
type: Parameter
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constant: true
value: 0.385

335386
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constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 335358

335398
type: Reaction
fast: false
reversible: true

335372
type: Species
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constant: false
boundary condition: false
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type: SpeciesReference
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335375
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boundary condition: false
has only substance units: false
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initial amount: NaN
in compartment: 335358

335365
type: Species
is version of: O00750
is: SBO:0000245
constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: NaN
in compartment: 335358

335385
type: Species
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is: SBO:0000245
constant: false
boundary condition: false
has only substance units: false
initial concentration: 1.0
initial amount: NaN
in compartment: 335358

335433
type: Parameter
is: SBO:0000009
constant: true
value: 0.3

335439
type: Parameter
is: SBO:0000002
constant: true
value: 80.0

335449
type: Parameter
is: SBO:0000002
constant: true
value: 0.1

335400
type: Reaction
reversible: true
fast: false

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335467
type: Parameter
is: SBO:0000002
constant: true
value: 3.45

335477
type: Parameter
is: SBO:0000002
constant: true
value: 6.57

335503
type: Parameter
is: SBO:0000009
constant: true
value: 4.64

335404
type: Reaction
fast: false
reversible: true

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335395
type: Reaction
fast: false
reversible: true

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type: SpeciesReference
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species: 335372

335454
type: Parameter
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constant: true
value: 6.77

335464
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constant: true
value: 23.0

335360
type: Species
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constant: false
boundary condition: false
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335489
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constant: true
value: 0.976

335370
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initial concentration: 0.0
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335493
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constant: true
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335359
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boundary condition: false
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initial amount: NaN
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335431
type: Parameter
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constant: true
value: 1.0

335447
type: Parameter
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constant: true
value: 5.09

335457
type: Parameter
is: SBO:0000002
constant: true
value: 1.18

335393
type: Reaction
fast: false
reversible: true

335367
type: Species
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constant: false
boundary condition: false
has only substance units: false
initial concentration: NaN
initial amount: NaN
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335434
type: Parameter
is: SBO:0000009
constant: true
value: 0.007

335444
type: Parameter
is: SBO:0000337
constant: true
value: 495.0

335462
type: Parameter
is: SBO:0000027
constant: true
value: 13.7

335472
type: Parameter
is: SBO:0000027
constant: true
value: 9.59

335390
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fast: false
reversible: true

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335478
type: Parameter
is: SBO:0000027
constant: true
value: 9.91

335405
type: Reaction
fast: false
reversible: true

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335482
type: Parameter
is: SBO:0000027
constant: true
value: 8.27

335487
type: Parameter
is: SBO:0000002
constant: true
value: 0.228

335497
type: Parameter
is: SBO:0000009
constant: true
value: 0.0333

335388
type: Reaction
fast: false
reversible: true

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type: SpeciesReference
stoichiometry: 1.0
species: 335359

335437
type: Parameter
is: SBO:0000009
constant: true
value: 0.2

335399
type: Reaction
reversible: true
fast: false

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type: SpeciesReference
stoichiometry: 1.0
species: 335377

335484
type: Parameter
is: SBO:0000027
constant: true
value: 8.81

335408
type: Reaction
fast: false
reversible: true

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type: SpeciesReference
stoichiometry: 1.0
species: 335387

335494
type: Parameter
is: SBO:0000009
constant: true
value: 3.76

335442
type: Parameter
is: SBO:0000282
constant: true
value: 0.3

335452
type: Parameter
is: SBO:0000009
constant: true
value: 0.745

335458
type: Parameter
is: SBO:0000027
constant: true
value: 30.3

335468
type: Parameter
is: SBO:0000027
constant: true
value: 18.6

335394
type: Reaction
fast: false
reversible: true

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type: SpeciesReference
stoichiometry: 1.0
species: 335371

ORG:
  orgname: Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
n:
  given: Jason M
  family: Haugh

335463
type: Parameter
is: SBO:0000002
constant: true
value: 1.65

335473
type: Parameter
is: SBO:0000002
constant: true
value: 4.2

335479
type: Parameter
is: SBO:0000002
constant: true
value: 0.167

335483
type: Parameter
is: SBO:0000002
constant: true
value: 31.9

335498
type: Parameter
is: SBO:0000009
constant: true
value: 2.34

335389
type: Reaction
fast: false
reversible: true

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type: SpeciesReference
stoichiometry: 1.0
species: 335362

335432
type: Parameter
is: SBO:0000282
constant: true
value: 1.5

335438
type: Parameter
is: SBO:0000009
constant: true
value: 0.005

335448
type: Parameter
is: SBO:0000009
constant: true
value: 1.0

W3 CDTF: Thu Jan 21 13:25:37 GMT 2010

ORG:
  orgname: EMBL-EBI
n:
  given: Vijayalakshmi
  family: Chelliah

W3 CDTF: Fri Jun 07 12:14:56 BST 2013