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notes: NCBS Curation Comments: This model shows the control mechanism of Jak-Stat pathway, here SOCS1 (Suppressor of cytokine signaling-I) was identified as the negative regulator of Jak and STAT signal transduction pathway. This is the knockout version of Jak-Stat pathway in this model the SOCS1 has been knocked out i.e it formation is not shown. The graphs are almost similar to the graphs as shown in the paper but STAT1n graph has some ambiguities. Thanks to Dr Satoshi Yamada for clarifying some of those ambiguities and providing the values used in simulations. Biomodels Curation Comments: The model reproduces the figures 2 (B,D,F,H,J,L,N) corresponding to JAK/STAT activation in SOCS1 knock out cells. The model was successfully tested on MathSBML This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2006 The BioModels Team. For more information see the terms of use .
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328053
type: LocalParameter
units: metaid_0000087
value: 5.0E-4

328029
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

328017
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000037

metaid_0000073
type: Reaction
kinetic law: 327788
product: 327776
reactant: 327764
reactant: 327752
is: GO:0005515
fast: false
reversible: false
name: STAT1c binding

327812
type: LocalParameter
units: metaid_0000087
value: 0.8

327800
type: LocalParameter
units: metaid_0000088
value: 0.008

327776
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000031

327764
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

327752
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000037

metaid_0000085
type: SBMLUnitsDef
unit: 325557
name: nanomoles

325557
type: SBMLUnit
exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE

metaid_0000078
type: Reaction
reactant: 328065
product: 328077
name: IFNRJ2 dephosphorylation
fast: false
kinetic law: 328113
product: 328089
product: 328101
is: GO:0005001
reversible: false

328065
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000037

328077
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

328125
type: LocalParameter
units: metaid_0000087
value: 0.003

328089
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000008

328101
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000029

metaid_0000074
type: Reaction
is: GO:0019902
fast: false
reactant: 327824
product: 327848
is: GO:0005515
name: SHP2 binding
reactant: 327836
reversible: false
kinetic law: 327860

327824
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

327848
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000036

metaid_0000036
type: Species
name: IFNRJ2_star_SHP2_STAT1c
boundary condition: false
in compartment: metaid_0000003
initial amount: NaN
has only substance units: false
constant: false
has part: P01572
has part: P42225
has part: P52332
has part: P15261
has part: P35235
initial concentration: 0.0

327836
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

327884
type: LocalParameter
units: metaid_0000087
value: 0.2

327872
type: LocalParameter
units: metaid_0000088
value: 0.001

metaid_0000021
type: Species
is: P42225
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000090
name: STAT1n_star

metaid_0000071
type: Reaction
kinetic law: 327655
product: 327643
reactant: 327631
fast: false
reversible: false
name: SOCS1 unbinding

327668
type: LocalParameter
units: metaid_0000087
value: 5.0E-4

327643
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000036

327631
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000031

metaid_0000054
type: Reaction
kinetic law: 326692
product: 326679
reactant: 326667
is: GO:0007262
fast: false
reversible: false
name: STAT1c-nuclear transport

326704
type: LocalParameter
units: metaid_0000087
value: 0.005

326679
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000020

326667
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000014

metaid_0000050
type: Reaction
kinetic law: 326437
product: 326425
product: 326413
reactant: 326401
fast: false
reversible: false
name: STAT1c dephosphorylation

326449
type: LocalParameter
units: metaid_0000087
value: 0.003

326425
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000017

326413
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

326401
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000018

metaid_0000027
type: Species
has only substance units: false
constant: false
name: mRNAn
initial concentration: 0.0
is: CHEBI:33699
in compartment: metaid_0000090
is: C00046
boundary condition: false
initial amount: NaN

metaid_0000069
type: Reaction
kinetic law: 327510
reactant: 327474
is: GO:0019902
product: 327498
is: GO:0005515
reactant: 327486
fast: false
reversible: false
name: SHP2 binding

327534
type: LocalParameter
units: metaid_0000087
value: 0.2

327522
type: LocalParameter
units: metaid_0000088
value: 0.001

327474
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000034

327498
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000031

327486
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

metaid_0000084
type: Reaction
kinetic law: 328509
product: 328497
reactant: 328485
reactant: 328473
is: GO:0019964
fast: false
reversible: false
name: IFNR-JAK binding

328533
type: LocalParameter
units: metaid_0000087
value: 0.05

328521
type: LocalParameter
units: metaid_0000088
value: 0.1

328497
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000007

328485
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000038

328473
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000005

metaid_0000032
type: Species
has part: P42225
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000003
name: STAT1c_star_STAT1c_star_PPX

metaid_0000067
type: Reaction
kinetic law: 327366
product: 327354
reactant: 327342
reactant: 327330
is: GO:0005515
fast: false
reversible: false
name: phosphorylated IFNRJ2-SOCS1 binding

327390
type: LocalParameter
units: metaid_0000087
value: 0.1

327378
type: LocalParameter
units: metaid_0000088
value: 0.02

327354
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000030

327342
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000029

327330
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

metaid_0000063
type: Reaction
kinetic law: 327186
product: 327174
reactant: 327162
is: GO:0006406
fast: false
reversible: false
name: mRNA transport to cytoplasm

327198
type: LocalParameter
units: metaid_0000087
value: 0.001

327174
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000028

327162
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000027

metaid_0000082
type: Reaction
kinetic law: 328365
product: 328353
reactant: 328341
reactant: 328329
is: GO:0005515
fast: false
reversible: false
name: SOCS1 binding

328389
type: LocalParameter
units: metaid_0000087
value: 0.1

328377
type: LocalParameter
units: metaid_0000088
value: 0.02

328353
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000031

328341
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000029

328329
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000036

metaid_0000089
type: SBMLUnitsDef
unit: 325666
unit: 325654
name: nM

325666
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE

325654
type: SBMLUnit
exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE

metaid_0000079
type: Reaction
kinetic law: 328161
product: 328149
reactant: 328137
fast: false
reversible: false
name: SOCS1 unbinding

328173
type: LocalParameter
units: metaid_0000087
value: 5.0E-4

328149
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

328137
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000030

metaid_0000075
type: Reaction
kinetic law: 327944
reversible: false
reactant: 327896
product: 327908
fast: false
is: GO:0043624
product: 327920
is: GO:0005001
product: 327932

327956
type: LocalParameter
units: metaid_0000087
value: 0.003

327896
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000036

327908
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

327920
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

327932
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000008

metaid_0000066
type: Reaction
kinetic law: 327306
reactant: 327294
is: GO:0044257
fast: false
reversible: false
name: SOCS1 degradation

327318
type: LocalParameter
units: metaid_0000087
value: 5.0E-4

327294
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000029

metaid_0000043
type: Reaction
kinetic law: 325967
product: 325955
reactant: 325943
reactant: 325931
is: GO:0005515
fast: false
reversible: false
name: Activated INFRJ2-STAT1c binding

325991
type: LocalParameter
units: metaid_0000087
value: 0.8

325979
type: LocalParameter
units: metaid_0000088
value: 0.008

325955
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

325943
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

325931
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

metaid_0000058
type: Reaction
kinetic law: 326946
product: 326934
reactant: 326922
reactant: 326910
is: GO:0019902
fast: false
reversible: false
name: PPN binding

326970
type: LocalParameter
units: metaid_0000087
value: 0.2

326958
type: LocalParameter
units: metaid_0000088
value: 0.001

326934
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000033

326922
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000022

326910
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000020

metaid_0000055
type: Reaction
kinetic law: 326741
product: 326728
reactant: 326716
is: GO:0007261
fast: false
reversible: false
name: Phosphorylated STAT1n dimerization

326765
type: LocalParameter
units: metaid_0000087
value: 0.1

326753
type: LocalParameter
units: metaid_0000088
value: 0.02

326728
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000020

326716
type: SpeciesReference
stoichiometry: 2.0
species: metaid_0000021

metaid_0000051
type: Reaction
kinetic law: 326499
product: 326486
reactant: 326473
reactant: 326461
is: GO:0019902
fast: false
reversible: false
name: PPX binding

326523
type: LocalParameter
units: metaid_0000087
value: 0.2

326511
type: LocalParameter
units: metaid_0000088
value: 0.001

326486
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000032

326473
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000017

326461
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000014

metaid_0000060
type: Reaction
kinetic law: 327078
product: 327066
reactant: 327054
reactant: 327042
is: GO:0007261
fast: false
reversible: false
name: STAT1n-phosphorylated STAT1n dimerization

327102
type: LocalParameter
units: metaid_0000087
value: 0.2

327090
type: LocalParameter
units: metaid_0000088
value: 2.0E-7

327066
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000025

327054
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000024

327042
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000021

W3 CDTF: Fri Jan 26 18:57:03 GMT 2007

metaid_0000041
type: Reaction
kinetic law: 325847
product: 325835
reactant: 325823
is: GO:0007171
fast: false
reversible: false
name: IFN-Receptor complex dimerization

325871
type: LocalParameter
units: metaid_0000087
value: 0.2

325859
type: LocalParameter
units: metaid_0000088
value: 0.04

325835
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000008

325823
type: SpeciesReference
stoichiometry: 2.0
species: metaid_0000007

metaid_0000056
type: Reaction
is: GO:0019902
reactant: 326789
product: 326801
name: PPN binding
reversible: false
reactant: 326777
is: GO:0005515
fast: false
kinetic law: 326813

326789
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000022

326801
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000023

326777
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000021

326837
type: LocalParameter
units: metaid_0000087
value: 0.2

326825
type: LocalParameter
units: metaid_0000088
value: 0.001

metaid_0000052
type: Reaction
kinetic law: 326571
product: 326559
product: 326547
reactant: 326535
is: GO:0042512
fast: false
reversible: false
name: STAT1c dimer dephosphorylation

326583
type: LocalParameter
units: metaid_0000087
value: 0.003

326559
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000017

326547
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000019

326535
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000032

ORG:
  orgname: California Institute of Technology
n:
  given: Harish
  family: Dharuri

W3 CDTF: Wed May 16 11:15:54 BST 2012