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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. Note: There are a few ambiguities in the paper like initial concentration of IFN and some reactions were missing in the paper that were employed for obtaining the results. The graphs are almost similar to the graphs as shown in the paper but still some ambiguities regarding the concentration are there. Thanks to Dr Satoshi Yamada for clarifying some of those ambiguities and providing the values used in simulations. Biomodels Curation Comments The model reproduces Fig 2 (A,C,E,G,I,K,M) of the paper. The set of equations present in the paper are inadequate to reproduce the figures mentioned . The model appears to have been fine tuned after correspondence between the curators at NCBS and the authors. There is however a slight discrepancy between the simulation results and the plots in the paper. The model was 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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species: metaid_0000037

metaid_0000072
type: Reaction
kinetic law: 298766
product: 298754
reactant: 298742
reactant: 298730
is: GO:0019902
fast: false
reversible: false
name: SHP2 binding

298790
type: LocalParameter
units: metaid_0000087
value: 0.2

298778
type: LocalParameter
units: metaid_0000088
value: 0.001

298754
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000037

298742
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

298730
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000030

metaid_0000048
type: Reaction
fast: false
is: GO:0005001
is: http://identifiers.org/ec-code/3.1.3.48
name: IFNJR2 dephosphorylation
product: 297274
product: 297286
kinetic law: 297298
reactant: 297262
reversible: false
is: R02585

297274
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

297286
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000008

297310
type: LocalParameter
units: metaid_0000087
value: 0.003

297262
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

metaid_0000047
type: Reaction
reversible: false
reactant: 297189
is: GO:0005515
product: 297213
name: SHP2 binding
is: GO:0019902
fast: false
kinetic law: 297225
reactant: 297201

297189
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

297213
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

297250
type: LocalParameter
units: metaid_0000087
value: 0.2

297237
type: LocalParameter
units: metaid_0000088
value: 0.001

297201
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

metaid_0000044
type: Reaction
name: STAT1c activation
is: GO:0007260
reactant: 296996
reversible: false
is: http://identifiers.org/ec-code/2.7.10.2
kinetic law: 297032
product: 297008
product: 297020
fast: false

296996
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

metaid_0000011
type: Species
in compartment: metaid_0000003
initial amount: NaN
constant: false
has part: O88507
has part: P42225
has part: P52332
has only substance units: false
initial concentration: 0.0
has part: P01572
name: IFNRJ2_star_STAT1c
boundary condition: false

297044
type: LocalParameter
units: metaid_0000087
value: 0.4

297008
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000012

297020
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

metaid_0000043
type: Reaction
kinetic law: 296960
product: 296948
reactant: 296936
reactant: 296924
is: GO:0005515
fast: false
reversible: false
name: Activated INFRJ2-STAT1c binding

296984
type: LocalParameter
units: metaid_0000087
value: 0.8

296972
type: LocalParameter
units: metaid_0000088
value: 0.008

296948
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

296936
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

296924
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

metaid_0000078
type: Reaction
kinetic law: 299163
product: 299139
product: 299151
name: IFNRJ2 dephosphorylation
product: 299127
reversible: false
reactant: 299115
is: GO:0005001
is: GO:0043624
fast: false

299176
type: LocalParameter
units: metaid_0000087
value: 0.003

299139
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000008

299151
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000029

299127
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

299115
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000037

metaid_0000084
type: Reaction
name: IFNR-JAK binding
is: GO:0005133
reactant: 299527
reversible: false
is: GO:0005515
kinetic law: 299563
reactant: 299539
fast: false
product: 299551

299527
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000005

299587
type: LocalParameter
units: metaid_0000087
value: 0.05

299575
type: LocalParameter
units: metaid_0000088
value: 0.1

299539
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000038

metaid_0000038
type: Species
in compartment: metaid_0000003
initial concentration: 0.0
constant: false
is: O88507
boundary condition: false
is: P01572
name: IFNR
has only substance units: false
initial amount: NaN

299551
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000007

metaid_0000083
type: Reaction
is: GO:0019964
fast: false
name: Interferon-receptor binding
kinetic law: 299491
is: GO:0004906
reversible: false
reactant: 299454
reactant: 299466
product: 299479

299515
type: LocalParameter
units: metaid_0000087
value: 0.02

299503
type: LocalParameter
units: metaid_0000088
value: 0.02

299454
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000004

299466
type: SpeciesReference
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species: metaid_0000035

299479
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000038

metaid_0000080
type: Reaction
kinetic law: 299273
product: 299261
reactant: 299249
reactant: 299236
is: GO:0005515
fast: false
reversible: false
name: SOCS1 binding

299297
type: LocalParameter
units: metaid_0000087
value: 0.1

299285
type: LocalParameter
units: metaid_0000088
value: 0.02

299261
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000034

299249
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000029

299236
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

metaid_0000041
type: Reaction
kinetic law: 296839
product: 296827
reactant: 296815
is: GO:0007171
fast: false
reversible: false
name: IFN-Receptor complex dimerization

296863
type: LocalParameter
units: metaid_0000087
value: 0.2

296851
type: LocalParameter
units: metaid_0000088
value: 0.04

296827
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000008

296815
type: SpeciesReference
stoichiometry: 2.0
species: metaid_0000007

metaid_0000064
type: Reaction
kinetic law: 298284
modifier: 298272
product: 298259
is: GO:0006412
fast: false
reversible: false
name: SOCS1 synthesis

298296
type: LocalParameter
units: metaid_0000087
value: 0.01

298259
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000029

metaid_0000076
type: Reaction
kinetic law: 299043
product: 299031
reactant: 299019
fast: false
reversible: false
name: SOCS1 unbinding

299055
type: LocalParameter
units: metaid_0000087
value: 5.0E-4

299031
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

299019
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000034

metaid_0000039
type: Reaction
fast: false
is: GO:0005515
is: GO:0005133
reversible: false
product: 296695
reactant: 296670
name: Receptor-JAK Binding
kinetic law: 296707
reactant: 296683

296695
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000006

296670
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000005

296731
type: LocalParameter
units: metaid_0000087
value: 0.05

296719
type: LocalParameter
units: metaid_0000088
value: 0.1

296683
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000004

metaid_0000085
type: SBMLUnitsDef
unit: 296550
name: nanomoles

296550
type: SBMLUnit
exponent: 1.0
scale: -9
multipler: 1.0
kind: MOLE

metaid_0000056
type: Reaction
kinetic law: 297802
product: 297790
reactant: 297778
reactant: 297766
is: GO:0019902
fast: false
reversible: false
name: PPN binding

297826
type: LocalParameter
units: metaid_0000087
value: 0.2

297814
type: LocalParameter
units: metaid_0000088
value: 0.001

297790
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000023

297778
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000022

297766
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000021

metaid_0000062
type: Reaction
kinetic law: 298175
modifier: 298163
product: 298151
is: GO:0006351
fast: false
reversible: false
name: Transcription

298199
type: LocalParameter
units: metaid_0000089
value: 400.0

298187
type: LocalParameter
units: metaid_0000086
value: 0.01

298151
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000027

metaid_0000061
type: Reaction
kinetic law: 298127
product: 298115
reactant: 298103
is: GO:0065002
fast: false
reversible: false
name: STAT1n transport to cytoplasm

298139
type: LocalParameter
units: metaid_0000087
value: 0.05

298115
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

298103
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000024

W3 CDTF: Wed Mar 07 18:40:22 GMT 2007

metaid_0000074
type: Reaction
kinetic law: 298911
product: 298899
reactant: 298887
reactant: 298875
is: GO:0019902
fast: false
reversible: false
name: SHP2 binding

298935
type: LocalParameter
units: metaid_0000087
value: 0.2

298923
type: LocalParameter
units: metaid_0000088
value: 0.001

298899
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000036

298887
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

298875
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000011

metaid_0000070
type: Reaction
product: 298610
product: 298646
fast: false
reactant: 298598
kinetic law: 298658
name: IFNRJ2 dephosphorylation
product: 298634
product: 298622
reversible: false
is: GO:0005001

298610
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000008

298646
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000015

298598
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000031

298670
type: LocalParameter
units: metaid_0000087
value: 0.003

298634
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

298622
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000029

metaid_0000049
type: Reaction
is: GO:0005515
reversible: false
reactant: 297334
product: 297346
name: Phosphorylated STAT1c-PPX binding
fast: false
reactant: 297322
kinetic law: 297358
is: GO:0019902

297334
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000017

297346
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000018

297322
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000012

297382
type: LocalParameter
units: metaid_0000087
value: 0.2

297370
type: LocalParameter
units: metaid_0000088
value: 0.001

metaid_0000068
type: Reaction
kinetic law: 298489
product: 298477
reactant: 298465
reactant: 298453
is: GO:0005515
fast: false
reversible: false
name: STAT1c binding

298514
type: LocalParameter
units: metaid_0000087
value: 0.8

298501
type: LocalParameter
units: metaid_0000088
value: 0.008

298477
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000034

298465
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

298453
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000030

metaid_0000045
type: Reaction
kinetic law: 297092
product: 297080
reactant: 297068
reactant: 297056
is: GO:0005515
fast: false
reversible: false
name: Activated IFNRJ2-STAT1c binding

297116
type: LocalParameter
units: metaid_0000087
value: 0.5

297104
type: LocalParameter
units: metaid_0000088
value: 0.005

297080
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000013

297068
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000009

297056
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000012

metaid_0000051
type: Reaction
kinetic law: 297490
product: 297478
reactant: 297466
reactant: 297454
is: GO:0019902
fast: false
reversible: false
name: PPX binding

297514
type: LocalParameter
units: metaid_0000087
value: 0.2

297502
type: LocalParameter
units: metaid_0000088
value: 0.001

297478
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000032

297466
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000017

297454
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000014

metaid_0000050
type: Reaction
kinetic law: 297430
product: 297418
product: 297406
reactant: 297394
is: GO:0042512
fast: false
reversible: false
name: STAT1c dephosphorylation

297442
type: LocalParameter
units: metaid_0000087
value: 0.003

297418
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000017

297406
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000010

297394
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000018

metaid_0000081
type: Reaction
kinetic law: 299345
product: 299333
reactant: 299321
reactant: 299309
is: GO:0005515
fast: false
reversible: false
name: SOCS1 binding

299369
type: LocalParameter
units: metaid_0000087
value: 0.1

299357
type: LocalParameter
units: metaid_0000088
value: 0.02

299333
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000037

299321
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000029

299309
type: SpeciesReference
stoichiometry: 1.0
species: metaid_0000016

W3 CDTF: Wed May 16 11:16:23 BST 2012

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