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

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BIOMD0000000094
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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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326449
units: metaid_0000087
value: 0.003
type: LocalParameter

327402
stoichiometry: 1.0
species: metaid_0000030
type: SpeciesReference

326124
units: metaid_0000087
value: 0.5
type: LocalParameter

metaid_0000061
kinetic law: 327138
product: 327126
reactant: 327114
is: GO:0065002
fast: false
reversible: false
name: STAT1n transport to cytoplasm
type: Reaction

326535
stoichiometry: 1.0
species: metaid_0000032
type: SpeciesReference

325678
stoichiometry: 1.0
species: metaid_0000005
type: SpeciesReference

328281
stoichiometry: 1.0
species: metaid_0000037
type: SpeciesReference

327342
stoichiometry: 1.0
species: metaid_0000029
type: SpeciesReference

327414
stoichiometry: 1.0
species: metaid_0000010
type: SpeciesReference

metaid_0000022
constant: false
boundary condition: false
has only substance units: false
initial concentration: 60.0
initial amount: NaN
in compartment: metaid_0000090
name: PPN
type: Species

327764
stoichiometry: 1.0
species: metaid_0000010
type: SpeciesReference

metaid_0000076
kinetic law: 327992
product: 327980
reactant: 327968
fast: false
reversible: false
name: SOCS1 unbinding
type: Reaction

metaid_0000049
kinetic law: 326365
product: 326353
reactant: 326341
reactant: 326329
is: GO:0019902
fast: false
reversible: false
name: Phosphorylated STAT1c-PPX binding
type: Reaction

metaid_0000036
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
type: Species
has part: P52332
has part: P15261
has part: P35235
initial concentration: 0.0

328185
stoichiometry: 1.0
species: metaid_0000011
type: SpeciesReference

325775
stoichiometry: 1.0
species: metaid_0000007
type: SpeciesReference

326377
units: metaid_0000088
value: 0.001
type: LocalParameter

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

metaid_0000023
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_PPN
type: Species

327114
stoichiometry: 1.0
species: metaid_0000024
type: SpeciesReference

328125
units: metaid_0000087
value: 0.003
type: LocalParameter

327680
stoichiometry: 1.0
species: metaid_0000030
type: SpeciesReference

326910
stoichiometry: 1.0
species: metaid_0000020
type: SpeciesReference

327174
stoichiometry: 1.0
species: metaid_0000028
type: SpeciesReference

326728
stoichiometry: 1.0
species: metaid_0000020
type: SpeciesReference

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

326112
units: metaid_0000088
value: 0.005
type: LocalParameter

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

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

326523
units: metaid_0000087
value: 0.2
type: LocalParameter

328497
stoichiometry: 1.0
species: metaid_0000007
type: SpeciesReference

326461
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

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

327595
stoichiometry: 1.0
species: metaid_0000015
type: SpeciesReference

328533
units: metaid_0000087
value: 0.05
type: LocalParameter

metaid_0000009
name: Activated IFNRJ complex
boundary condition: false
has part: P01572
initial concentration: 0.0
constant: false
has only substance units: false
in compartment: metaid_0000003
initial amount: NaN
type: Species
has part: P52332
has part: P15261

326825
units: metaid_0000088
value: 0.001
type: LocalParameter

327728
units: metaid_0000088
value: 0.001
type: LocalParameter

metaid_0000034
constant: false
initial amount: NaN
has part: P52332
has part: P15261
has part: P42225
type: Species
in compartment: metaid_0000003
has part: O35716
has only substance units: false
initial concentration: 0.0
boundary condition: false
has part: P01572
name: IFNRJ2_star_SOCS1_STAT1c

327752
stoichiometry: 1.0
species: metaid_0000037
type: SpeciesReference

326028
stoichiometry: 1.0
species: metaid_0000009
type: SpeciesReference

metaid_0000024
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
type: Species

327330
stoichiometry: 1.0
species: metaid_0000009
type: SpeciesReference

326753
units: metaid_0000088
value: 0.02
type: LocalParameter

326088
stoichiometry: 1.0
species: metaid_0000013
type: SpeciesReference

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

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

metaid_0000064
kinetic law: 327234
modifier: 327222
product: 327210
is: GO:0006412
fast: false
reversible: false
name: SOCS1 synthesis
type: Reaction

328029
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

325835
stoichiometry: 1.0
species: metaid_0000008
type: SpeciesReference

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

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

326777
stoichiometry: 1.0
species: metaid_0000021
type: SpeciesReference

328341
stoichiometry: 1.0
species: metaid_0000029
type: SpeciesReference

328089
stoichiometry: 1.0
species: metaid_0000008
type: SpeciesReference

326716
stoichiometry: 2.0
species: metaid_0000021
type: SpeciesReference

325581
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE
type: SBMLUnit

326172
units: metaid_0000088
value: 0.02
type: LocalParameter

326559
stoichiometry: 1.0
species: metaid_0000017
type: SpeciesReference

metaid_0000031
has part: P01572
initial amount: NaN
type: Species
has part: P52332
in compartment: metaid_0000003
initial concentration: 0.0
has only substance units: false
has part: P35235
has part: O35716
constant: false
has part: P15261
has part: P42225
name: IFNRJ2_star_SHP2_SOCS1_STAT1c
boundary condition: false

328317
units: metaid_0000087
value: 0.1
type: LocalParameter

326655
units: metaid_0000087
value: 0.2
type: LocalParameter

metaid_0000011
initial amount: NaN
has part: P01572
boundary condition: false
has part: P52332
in compartment: metaid_0000003
constant: false
has only substance units: false
type: Species
name: IFNRJ2_star_STAT1c
has part: P42225
has part: P15261
initial concentration: 0.0

327378
units: metaid_0000088
value: 0.02
type: LocalParameter

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

327162
stoichiometry: 1.0
species: metaid_0000027
type: SpeciesReference

metaid_0000080
kinetic law: 328221
product: 328209
reactant: 328197
reactant: 328185
is: GO:0005515
fast: false
reversible: false
name: SOCS1 binding
type: Reaction

metaid_0000090
is: GO:0005634
constant: true
size: 1.0
spatial dimensions: 3.0
name: nucleus
type: Compartment

328257
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

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

327800
units: metaid_0000088
value: 0.008
type: LocalParameter

326861
stoichiometry: 1.0
species: metaid_0000024
type: SpeciesReference

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

328017
stoichiometry: 1.0
species: metaid_0000037
type: SpeciesReference

327390
units: metaid_0000087
value: 0.1
type: LocalParameter

325823
stoichiometry: 2.0
species: metaid_0000007
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

328305
units: metaid_0000088
value: 0.02
type: LocalParameter

327066
stoichiometry: 1.0
species: metaid_0000025
type: SpeciesReference

327450
units: metaid_0000088
value: 0.008
type: LocalParameter

325739
units: metaid_0000087
value: 0.05
type: LocalParameter

metaid_0000012
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
type: Species

326208
stoichiometry: 1.0
species: metaid_0000009
type: SpeciesReference

325883
stoichiometry: 1.0
species: metaid_0000008
type: SpeciesReference

327558
stoichiometry: 1.0
species: metaid_0000008
type: SpeciesReference

metaid_0000072
type: Reaction
fast: false
product: 327704
name: SHP2 binding
reactant: 327680
is: GO:0019902
reactant: 327692
is: GO:0005515
kinetic law: 327716
reversible: false

327740
units: metaid_0000087
value: 0.2
type: LocalParameter

326704
units: metaid_0000087
value: 0.005
type: LocalParameter

326184
units: metaid_0000087
value: 0.1
type: LocalParameter

326547
stoichiometry: 1.0
species: metaid_0000019
type: SpeciesReference

328329
stoichiometry: 1.0
species: metaid_0000036
type: SpeciesReference

328004
units: metaid_0000087
value: 5.0E-4
type: LocalParameter

326765
units: metaid_0000087
value: 0.1
type: LocalParameter

325812
units: metaid_0000087
value: 0.02
type: LocalParameter

328245
units: metaid_0000087
value: 0.1
type: LocalParameter

326353
stoichiometry: 1.0
species: metaid_0000018
type: SpeciesReference

327968
stoichiometry: 1.0
species: metaid_0000034
type: SpeciesReference

326667
stoichiometry: 1.0
species: metaid_0000014
type: SpeciesReference

326269
stoichiometry: 1.0
species: metaid_0000016
type: SpeciesReference

327150
units: metaid_0000087
value: 0.05
type: LocalParameter

328101
stoichiometry: 1.0
species: metaid_0000029
type: SpeciesReference

327643
stoichiometry: 1.0
species: metaid_0000036
type: SpeciesReference

326619
stoichiometry: 1.0
species: metaid_0000019
type: SpeciesReference

metaid_0000020
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_STAT1n_star
type: Species

328197
stoichiometry: 1.0
species: metaid_0000029
type: SpeciesReference

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

metaid_0000040
is: GO:0004906
fast: false
reactant: 325751
product: 325775
is: GO:0019964
reactant: 325763
kinetic law: 325788
type: Reaction
name: Interferon-Receptor Binding
reversible: false

metaid_0000030
name: IFNRJ2_star_SOCS1
has part: P52332
initial concentration: 0.0
has part: P01572
type: Species
has part: P15261
initial amount: NaN
in compartment: metaid_0000003
has only substance units: false
has part: O35716
boundary condition: false
constant: false

325800
units: metaid_0000088
value: 0.02
type: LocalParameter

metaid_0000070
name: IFNRJ2 dephosphorylation
reversible: false
type: Reaction
product: 327571
product: 327583
kinetic law: 327607
product: 327558
product: 327595
fast: false
reactant: 327546
is: GO:0005001

326801
stoichiometry: 1.0
species: metaid_0000023
type: SpeciesReference

metaid_0000010
is: P42225
boundary condition: false
is: IPR001217
name: STAT1c
initial concentration: 1000.0
initial amount: NaN
in compartment: metaid_0000003
has only substance units: false
constant: false
type: Species

325727
units: metaid_0000088
value: 0.1
type: LocalParameter

325763
stoichiometry: 1.0
species: metaid_0000035
type: SpeciesReference

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

327354
stoichiometry: 1.0
species: metaid_0000030
type: SpeciesReference

325871
units: metaid_0000087
value: 0.2
type: LocalParameter

orgname: California Institute of Technology

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

n:
  given: Harish
  family: Dharuri