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

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299031
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

298091
units: metaid_0000087
value: 0.2
type: LocalParameter

metaid_0000048
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
type: Reaction

metaid_0000054
kinetic law: 297682
product: 297670
reactant: 297658
is: GO:0007262
fast: false
reversible: false
name: STAT1c-nuclear transport
type: Reaction

298514
units: metaid_0000087
value: 0.8
type: LocalParameter

297237
units: metaid_0000088
value: 0.001
type: LocalParameter

296912
units: metaid_0000087
value: 0.005
type: LocalParameter

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

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

metaid_0000007
type: Species
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in compartment: metaid_0000003
has part: P52332
has part: O88507
has only substance units: false
constant: false
boundary condition: false
name: Interferon-Receptor-JAK complex
initial amount: NaN
initial concentration: 0.0

299297
units: metaid_0000087
value: 0.1
type: LocalParameter

297250
units: metaid_0000087
value: 0.2
type: LocalParameter

296743
stoichiometry: 1.0
species: metaid_0000006
type: SpeciesReference

297994
stoichiometry: 1.0
species: metaid_0000022
type: SpeciesReference

297177
units: metaid_0000087
value: 0.1
type: LocalParameter

297982
stoichiometry: 1.0
species: metaid_0000025
type: SpeciesReference

metaid_0000034
has only substance units: false
has part: O88507
has part: P01572
boundary condition: false
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initial amount: NaN
has part: P42225
type: Species
has part: P52332
in compartment: metaid_0000003
name: IFNRJ2_star_SOCS1_STAT1c
constant: false

296598
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

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

297958
units: metaid_0000087
value: 0.2
type: LocalParameter

metaid_0000067
kinetic law: 298416
product: 298404
reactant: 298392
reactant: 298380
is: GO:0005515
fast: false
reversible: false
name: phosphorylated IFNRJ2-SOCS1 binding
type: Reaction

299406
stoichiometry: 1.0
species: metaid_0000031
type: SpeciesReference

296827
stoichiometry: 1.0
species: metaid_0000008
type: SpeciesReference

299127
stoichiometry: 1.0
species: metaid_0000015
type: SpeciesReference

metaid_0000014
is: 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
type: Species

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

298477
stoichiometry: 1.0
species: metaid_0000034
type: SpeciesReference

298815
stoichiometry: 1.0
species: metaid_0000010
type: SpeciesReference

298694
stoichiometry: 1.0
species: metaid_0000036
type: SpeciesReference

metaid_0000028
type: Species
constant: false
has only substance units: false
boundary condition: false
initial amount: NaN
in compartment: metaid_0000003
is: C00046
name: mRNAc
is: CHEBI:33699
initial concentration: 0.0

metaid_0000053
kinetic law: 297622
product: 297610
reactant: 297598
reactant: 297586
is: GO:0005515
fast: false
reversible: false
name: STAT1c-phosphorylated STAT1c binding
type: Reaction

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

297742
units: metaid_0000088
value: 0.02
type: LocalParameter

297526
stoichiometry: 1.0
species: metaid_0000032
type: SpeciesReference

metaid_0000008
has part: P52332
type: Species
name: IFNRJ dimer
boundary condition: false
has part: P01572
initial concentration: 0.0
in compartment: metaid_0000003
constant: false
initial amount: NaN
has part: O88507
has only substance units: false

299551
stoichiometry: 1.0
species: metaid_0000007
type: SpeciesReference

296683
stoichiometry: 1.0
species: metaid_0000004
type: SpeciesReference

297322
stoichiometry: 1.0
species: metaid_0000012
type: SpeciesReference

299261
stoichiometry: 1.0
species: metaid_0000034
type: SpeciesReference

298211
stoichiometry: 1.0
species: metaid_0000027
type: SpeciesReference

metaid_0000033
has part: 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_STAT1n_star_PPN
type: Species

298501
units: metaid_0000088
value: 0.008
type: LocalParameter

297116
units: metaid_0000087
value: 0.5
type: LocalParameter

297658
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

298923
units: metaid_0000088
value: 0.001
type: LocalParameter

298187
units: metaid_0000086
value: 0.01
type: LocalParameter

298610
stoichiometry: 1.0
species: metaid_0000008
type: SpeciesReference

metaid_0000029
has only substance units: false
name: SOCS1
initial amount: NaN
initial concentration: 0.0
is: IPR001496
in compartment: metaid_0000003
type: Species
is: O35716
constant: false
boundary condition: false

296586
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND
type: SBMLUnit

297694
units: metaid_0000087
value: 0.005
type: LocalParameter

297262
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

297165
units: metaid_0000088
value: 0.02
type: LocalParameter

metaid_0000019
is: P42225
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid_0000003
name: STAT1c_STAT1c_star
type: Species

298778
units: metaid_0000088
value: 0.001
type: LocalParameter

296863
units: metaid_0000087
value: 0.2
type: LocalParameter

299309
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

297201
stoichiometry: 1.0
species: metaid_0000009
type: SpeciesReference

298019
units: metaid_0000087
value: 0.005
type: LocalParameter

metaid_0000042
kinetic law: 296900
reversible: false
is: R02584
name: INF-Receptor complex activation
reactant: 296875
is: GO:0004713
type: Reaction
is: http://identifiers.org/ec-code/2.7.10.2
product: 296887
fast: false

299224
units: metaid_0000087
value: 5.0E-4
type: LocalParameter

298031
stoichiometry: 1.0
species: metaid_0000021
type: SpeciesReference

297068
stoichiometry: 1.0
species: metaid_0000009
type: SpeciesReference

metaid_0000032
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
type: Species

299575
units: metaid_0000088
value: 0.1
type: LocalParameter

298718
units: metaid_0000087
value: 5.0E-4
type: LocalParameter

metaid_0000085
unit: 296550
name: nanomoles
type: SBMLUnitsDef

298959
stoichiometry: 1.0
species: metaid_0000010
type: SpeciesReference

299321
stoichiometry: 1.0
species: metaid_0000029
type: SpeciesReference

298983
stoichiometry: 1.0
species: metaid_0000008
type: SpeciesReference

297718
stoichiometry: 1.0
species: metaid_0000020
type: SpeciesReference

297514
units: metaid_0000087
value: 0.2
type: LocalParameter

297478
stoichiometry: 1.0
species: metaid_0000032
type: SpeciesReference

298875
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

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

metaid_0000069
is: GO:0019902
reactant: 298538
fast: false
reversible: false
reactant: 298526
type: Reaction
name: SHP2 binding
product: 298550
is: GO:0005515
kinetic law: 298562

297754
units: metaid_0000087
value: 0.1
type: LocalParameter

296719
units: metaid_0000088
value: 0.1
type: LocalParameter

298428
units: metaid_0000088
value: 0.02
type: LocalParameter

metaid_0000031
initial concentration: 0.0
initial amount: NaN
name: IFNRJ2_star_SHP2_SOCS1_STAT1c
has part: P52332
has only substance units: false
type: Species
has part: P42225
has part: P35235
constant: false
has part: O88507
has part: P01572
in compartment: metaid_0000003
has part: O35716
boundary condition: false

299139
stoichiometry: 1.0
species: metaid_0000008
type: SpeciesReference

metaid_0000059
kinetic law: 298007
product: 297994
product: 297982
reactant: 297970
is: GO:0042512
fast: false
reversible: false
name: STAT1n dephosphorylation
type: Reaction

298441
units: metaid_0000087
value: 0.1
type: LocalParameter

299503
units: metaid_0000088
value: 0.02
type: LocalParameter

298296
units: metaid_0000087
value: 0.01
type: LocalParameter

metaid_0000088
unit: 296634
unit: 296622
unit: 296610
name: nM_inv_sec_inv
type: SBMLUnitsDef

297274
stoichiometry: 1.0
species: metaid_0000015
type: SpeciesReference

296574
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

298550
stoichiometry: 1.0
species: metaid_0000031
type: SpeciesReference

metaid_0000017
constant: false
boundary condition: false
has only substance units: false
initial concentration: 50.0
initial amount: NaN
in compartment: metaid_0000003
name: PPX
type: Species

296767
stoichiometry: 1.0
species: metaid_0000007
type: SpeciesReference

299587
units: metaid_0000087
value: 0.05
type: LocalParameter

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

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

298802
stoichiometry: 1.0
species: metaid_0000037
type: SpeciesReference

metaid_0000058
kinetic law: 297934
product: 297922
reactant: 297910
reactant: 297898
is: GO:0019902
fast: false
reversible: false
name: PPN binding
type: Reaction

296851
units: metaid_0000088
value: 0.04
type: LocalParameter

298380
stoichiometry: 1.0
species: metaid_0000009
type: SpeciesReference

298368
units: metaid_0000087
value: 5.0E-4
type: LocalParameter

298199
units: metaid_0000089
value: 400.0
type: LocalParameter

297406
stoichiometry: 1.0
species: metaid_0000010
type: SpeciesReference

metaid_0000030
has only substance units: false
initial concentration: 0.0
name: IFNRJ2_star_SOCS1
in compartment: metaid_0000003
has part: O88507
type: Species
boundary condition: false
has part: P01572
has part: P52332
constant: false
has part: O35716
initial amount: NaN

297213
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

299236
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

metaid_0000003
is: GO:0005737
constant: true
size: 1.0
spatial dimensions: 3.0
name: cytoplasm
type: Compartment

297466
stoichiometry: 1.0
species: metaid_0000017
type: SpeciesReference

metaid_0000087
unit: 296598
name: sec_inv
type: SBMLUnitsDef

298947
stoichiometry: 1.0
species: metaid_0000036
type: SpeciesReference

297706
stoichiometry: 2.0
species: metaid_0000021
type: SpeciesReference

298971
stoichiometry: 1.0
species: metaid_0000015
type: SpeciesReference

298103
stoichiometry: 1.0
species: metaid_0000024
type: SpeciesReference

297502
units: metaid_0000088
value: 0.001
type: LocalParameter

metaid_0000018
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_PPX
type: Species

296803
units: metaid_0000087
value: 0.02
type: LocalParameter

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

298453
stoichiometry: 1.0
species: metaid_0000030
type: SpeciesReference

298863
units: metaid_0000087
value: 0.8
type: LocalParameter

metaid_0000057
kinetic law: 297874
product: 297862
product: 297850
reactant: 297838
is: GO:0042512
fast: false
reversible: false
name: STAT1n dephosphorylation
type: Reaction

metaid_0000004
is: O88507
constant: false
boundary condition: false
has only substance units: false
initial concentration: 10.0
initial amount: NaN
in compartment: metaid_0000003
name: Receptor
type: Species

297766
stoichiometry: 1.0
species: metaid_0000021
type: SpeciesReference

given: Harish
family: Dharuri

orgname: California Institute of Technology

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