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536837
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538219
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539395
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537397
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539397
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156288
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538214
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537887
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162209
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135202
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539396
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537661
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538327
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539398
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154209
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538211
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537886
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539399
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540163
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539519
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168185
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538325
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538212
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535110
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537398
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538771
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539824
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538666
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537883
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536840
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158406
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540024
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537412
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166346
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536900
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537884
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539823
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540154
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154995
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540026
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540156
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539514
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538903
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137120
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540157
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540020
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538902
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539512
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539939
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158129
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536903
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536046
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539511
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540159
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540022
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537668
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162787
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539786
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535119
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536158
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539938
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536902
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536909
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538088
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536272
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ORG:
  orgname: Humboldt University Berlin
n:
  given: Clemens
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536908
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538086
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535323
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boundary condition: true
has only substance units: false
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initial amount: NaN
in compartment: 534968
name: GENE_P_Eve
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539788
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146810
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535869
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name: PROTEIN_M_Gcad
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537292
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modifier: 150795
product: 150783
reactant: 150771
fast: false
reversible: false
name: PROTEIN_M_VEGFR_degradation
type: Reaction

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

536155
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boundary condition: false
has only substance units: false
initial concentration: 0.0
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in compartment: 534968
name: PROTEIN_P_Hox
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538777
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type: LocalParameter

539935
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type: LocalParameter

536846
modifier: 132681
name: GENE_E_Erg_transcription
modifier: 132669
reversible: false
modifier: 132693
kinetic law: 132706
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reactant: 132644
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538085
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535320
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boundary condition: true
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 534968
name: GENE_P_Ets1
type: Species

539678
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type: LocalParameter

166118
stoichiometry: 1.0
species: 535974
type: SpeciesReference

536906
product: 135721
modifier: 135745
modifier: 135757
name: GENE_E_z13_transcription
reactant: 135709
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reversible: false
fast: false
kinetic law: 135769

155319
stoichiometry: 1.0
species: 535524
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537293
kinetic law: 150869
product: 150856
reactant: 150844
reactant: 150832
reactant: 150820
fast: false
reversible: false
name: PROTEIN_M_VEGFSignal_accociation
type: Reaction

539934
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type: LocalParameter

538776
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type: LocalParameter

536049
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boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 534968
name: PROTEIN_P_Blimp1
type: Species

149999
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species: 535941
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536845
kinetic law: 132632
modifier: 132620
modifier: 132608
product: 132596
reactant: 132584
fast: false
reversible: false
name: GENE_E_Endo16_transcription
type: Reaction

539829
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type: LocalParameter

539677
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type: LocalParameter

148121
stoichiometry: 1.0
species: 535818
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136083
stoichiometry: 1.0
species: 536488
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540028
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type: LocalParameter

539671
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type: LocalParameter

539672
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type: LocalParameter

164819
stoichiometry: 1.0
species: 536811
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169758
stoichiometry: 1.0
species: 536811
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537520
kinetic law: 157381
modifier: 157369
product: 157357
reactant: 157345
fast: false
reversible: false
name: mRNA_E_FoxO_translation
type: Reaction

536278
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boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 534968
name: PROTEIN_P_VEGFSignal
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538662
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type: LocalParameter

535326
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boundary condition: true
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 534968
name: GENE_P_Ficolin
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539933
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type: LocalParameter

538083
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161822
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species: 536497
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538775
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167705
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species: 536811
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537295
kinetic law: 150931
product: 150919
product: 150906
product: 150894
reactant: 150881
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reversible: false
name: PROTEIN_M_VEGFSignal_dissociation
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170097
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species: 536755
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539670
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type: LocalParameter

539932
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144137
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species: 535545
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536843
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reversible: false
product: 132524
modifier: 132560
kinetic law: 132572
type: Reaction
name: GENE_E_ES_transcription
fast: false
reactant: 132512
modifier: 132548

145089
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species: 535602
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540029
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538661
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537296
kinetic law: 150980
modifier: 150968
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reactant: 150943
fast: false
reversible: false
name: PROTEIN_M_Wnt8_degradation
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537521
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modifier: 157417
product: 157405
reactant: 157393
fast: false
reversible: false
name: mRNA_E_FvMo_degradation
type: Reaction

538774
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type: LocalParameter

536152
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boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 534968
name: PROTEIN_P_Hnf6
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538082
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type: LocalParameter

139134
stoichiometry: 1.0
species: 536611
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147964
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species: 535812
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539931
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type: LocalParameter

539674
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538660
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538773
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536842
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modifier: 132488
modifier: 132476
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reactant: 132451
fast: false
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name: GENE_E_Dri_transcription
type: Reaction

169337
stoichiometry: 1.0
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161257
stoichiometry: 1.0
species: 536811
type: SpeciesReference

539930
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539673
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536275
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boundary condition: false
has only substance units: false
initial concentration: 0.0
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in compartment: 534968
name: PROTEIN_P_VEGFR
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538080
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537298
kinetic law: 151016
modifier: 151004
reactant: 150992
fast: false
reversible: false
name: PROTEIN_M_cB_a_degradation
type: Reaction

153404
stoichiometry: 1.0
species: 536811
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538772
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type: LocalParameter

ORG:
  orgname: EMBL-EBI
n:
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  family: Endler

535551
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boundary condition: false
has only substance units: false
initial concentration: 0.0
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name: PROTEIN_E_CAPK
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538227
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537535
kinetic law: 157865
modifier: 157853
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reversible: false
name: mRNA_E_Gcm_translation
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538332
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163316
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137240
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537278
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modifier: 150361
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name: PROTEIN_M_SuH_degradation
type: Reaction

535773
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has only substance units: false
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name: PROTEIN_E_Wnt8
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167933
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168041
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species: 536079
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539692
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539694
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538333
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152837
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species: 536811
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537277
kinetic law: 150325
product: 150313
product: 150301
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fast: false
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name: PROTEIN_M_SuHN_dissociation
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538228
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136891
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140583
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133165
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species: 535023
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539693
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167657
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species: 536064
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538334
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538229
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169565
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species: 536811
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145908
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species: 536811
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539690
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135649
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species: 536470
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144656
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164579
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147233
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537536
kinetic law: 157913
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product: 157889
reactant: 157877
fast: false
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name: mRNA_E_Gelsolin_degradation
type: Reaction

538335
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538091
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type: LocalParameter

535407
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boundary condition: true
has only substance units: false
initial concentration: 0.0
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in compartment: 534968
name: GENE_P_Sm50
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537275
kinetic law: 150277
product: 150265
reactant: 150253
reactant: 150241
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name: PROTEIN_M_SuHN_accociation
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171170
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species: 536811
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172559
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species: 536811
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535887
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has only substance units: false
initial concentration: 0.0
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in compartment: 534968
name: PROTEIN_M_HesC
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539691
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140149
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species: 536668
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135079
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species: 535098
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536825
kinetic law: 131753
product: 131741
reactant: 131729
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name: E_UbiqSoxB1_Hill_Kinetic
type: Reaction

537539
kinetic law: 158009
modifier: 157997
product: 157985
reactant: 157973
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reversible: false
name: mRNA_E_HesC_degradation
type: Reaction

538768
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536290
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boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 534968
name: PROTEIN_P_frizzled_i
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164134
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species: 536569
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535401
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has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 534968
name: GENE_P_Sm27
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538769
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535554
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has only substance units: false
initial concentration: 0.0
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name: PROTEIN_E_CyP
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537538
kinetic law: 157961
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product: 157937
reactant: 157925
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reversible: false
name: mRNA_E_Gelsolin_translation
type: Reaction

142495
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species: 535395
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536827
kinetic law: 131789
product: 131777
reactant: 131765
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131655
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535557
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initial concentration: 0.0
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in compartment: 534968
name: PROTEIN_E_Delta
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535404
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initial concentration: 0.0
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in compartment: 534968
name: GENE_P_Sm30
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143401
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species: 535431
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538330
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140355
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species: 536680
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538331
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146461
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species: 535692
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151040
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species: 536811
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535770
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name: PROTEIN_E_VEGFSignal
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536828
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536293
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name: PROTEIN_P_nBTCF
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133311
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540043
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168461
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species: 536704
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540172
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538908
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538659
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144377
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species: 535557
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537878
kinetic law: 168881
modifier: 168869
product: 168857
reactant: 168845
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name: mRNA_P_GataC_degradation
type: Reaction

161112
stoichiometry: 1.0
species: 535776
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537652
kinetic law: 161618
modifier: 161606
product: 161594
reactant: 161582
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name: mRNA_M_Bra_translation
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159716
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species: 536811
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153271
stoichiometry: 1.0
species: 536176
type: SpeciesReference

540171
value: 2.0
type: LocalParameter

W3 CDTF: Wed Aug 31 20:46:06 BST 2011

540042
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type: LocalParameter

156973
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species: 535584
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538909
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537877
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modifier: 168821
product: 168809
reactant: 168797
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name: mRNA_P_FvMo_translation
type: Reaction

538220
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157021
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species: 536811
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164243
stoichiometry: 1.0
species: 536811
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540170
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134119
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species: 535065
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540041
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538221
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157503
stoichiometry: 1.0
species: 536811
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538906
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537389
kinetic law: 153909
product: 153897
reactant: 153885
reactant: 153873
fast: false
reversible: false
name: PROTEIN_P_SuHN_accociation
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158562
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species: 536811
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160763
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species: 536467
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538907
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540040
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171473
stoichiometry: 1.0
species: 536811
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159910
stoichiometry: 1.0
species: 536811
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538222
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537388
kinetic law: 153861
modifier: 153849
product: 153837
reactant: 153825
fast: false
reversible: false
name: PROTEIN_P_SoxC_degradation
type: Reaction

537653
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modifier: 161654
product: 161642
reactant: 161630
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reversible: false
name: mRNA_M_Brn_degradation
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166551
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species: 536811
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154354
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species: 536263
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145427
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species: 535713
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539506
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162365
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species: 535830
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157925
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species: 536811
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540176
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537874
kinetic law: 168737
modifier: 168725
product: 168713
reactant: 168701
fast: false
reversible: false
name: mRNA_P_FoxO_translation
type: Reaction

538336
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538223
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152017
stoichiometry: 1.0
species: 536085
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539507
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type: LocalParameter

535776
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boundary condition: false
has only substance units: false
initial concentration: 10.0
initial amount: NaN
in compartment: 534968
name: PROTEIN_E_cB
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535881
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boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 534968
name: PROTEIN_M_GroTCF
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540175
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537386
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modifier: 153801
product: 153789
reactant: 153777
fast: false
reversible: false
name: PROTEIN_P_SoxB1_degradation
type: Reaction

538337
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type: LocalParameter

538224
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167500
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species: 536674
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537425
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product: 155043
reactant: 155031
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name: P_Ets1_Hill_Kinetic
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535779
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initial amount: NaN
in compartment: 534968
name: PROTEIN_E_frizzled_a
type: Species

W3 CDTF: Fri Jan 15 16:34:00 GMT 2010

540174
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type: LocalParameter

535884
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boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 534968
name: PROTEIN_M_GroTFC
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538338
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type: LocalParameter

535101
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boundary condition: true
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 534968
name: GENE_E_SoxB1
type: Species

537650
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reactant: 161534
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name: mRNA_M_Bra_degradation
type: Reaction

154910
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537385
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name: PROTEIN_P_Snail_degradation
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537428
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reactant: 155103
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name: P_L1_Hill_Kinetic
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143704
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538225
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152414
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species: 536116
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539509
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156107
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species: 535554
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540173
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537383
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product: 153693
reactant: 153681
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name: PROTEIN_P_Sm50_degradation
type: Reaction

146053
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537875
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modifier: 168773
product: 168761
reactant: 168749
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name: mRNA_P_FvMo_degradation
type: Reaction

538339
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137977
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species: 536566
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537427
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product: 155079
reactant: 155067
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name: P_Gcad_Hill_Kinetic
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161919
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species: 536500
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538226
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145896
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537659
kinetic law: 161859
modifier: 161847
product: 161835
reactant: 161822
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name: mRNA_M_CyP_degradation
type: Reaction

538800
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538913
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135793
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species: 536479
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537421
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product: 154910
reactant: 154898
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name: PROTEIN_P_nBTCF_accociation
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538652
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540167
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163472
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species: 536811
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540038
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535998
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boundary condition: false
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initial concentration: 0.0
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in compartment: 534968
name: PROTEIN_M_UbiqEts1
type: Species

538912
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166057
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539794
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155151
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153127
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species: 536811
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136735
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537395
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name: PROTEIN_P_Tel_degradation
type: Reaction

538651
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537422
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product: 154958
product: 154946
reactant: 154934
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reversible: false
name: PROTEIN_P_nBTCF_dissociation
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540039
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537394
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reactant: 154017
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reversible: false
name: PROTEIN_P_TBr_degradation
type: Reaction

173630
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initial value: true
type: Trigger

539502
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537896
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notes: This a model from the article: Monte Carlo analysis of an ODE Model of the Sea Urchin Endomesoderm Network. Kühn C, Wierling C, Kühn A, Klipp E, Panopoulou G, Lehrach H, Poustka AJ. BMC Syst Biol. 2009 Aug 23;3:83. 19698179 , Abstract: BACKGROUND: Gene Regulatory Networks (GRNs) control the differentiation, specification and function of cells at the genomic level. The levels of interactions within large GRNs are of enormous depth and complexity. Details about many GRNs are emerging, but in most cases it is unknown to what extent they control a given process, i.e. the grade of completeness is uncertain. This uncertainty stems from limited experimental data, which is the main bottleneck for creating detailed dynamical models of cellular processes. Parameter estimation for each node is often infeasible for very large GRNs. We propose a method, based on random parameter estimations through Monte-Carlo simulations to measure completeness grades of GRNs. RESULTS: We developed a heuristic to assess the completeness of large GRNs, using ODE simulations under different conditions and randomly sampled parameter sets to detect parameter-invariant effects of perturbations. To test this heuristic, we constructed the first ODE model of the whole sea urchin endomesoderm GRN, one of the best studied large GRNs. We find that nearly 48% of the parameter-invariant effects correspond with experimental data, which is 65% of the expected optimal agreement obtained from a submodel for which kinetic parameters were estimated and used for simulations. Randomized versions of the model reproduce only 23.5% of the experimental data. CONCLUSION: The method described in this paper enables an evaluation of network topologies of GRNs without requiring any parameter values. The benefit of this method is exemplified in the first mathematical analysis of the complete Endomesoderm Network Model. The predictions we provide deliver candidate nodes in the network that are likely to be erroneous or miss u…
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stoichiometry: 1.0
species: 535806
type: SpeciesReference

539968
value: 0.119
type: LocalParameter

538940
value: 1.0
type: LocalParameter

536746
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 534968
name: mRNA_P_L1
type: Species

536891
modifier: 135042
modifier: 134994
reactant: 134945
modifier: 135030
product: 134957
kinetic law: 135067
reversible: false
modifier: 135055
name: GENE_E_Sm50_transcription
modifier: 134969
type: Reaction
modifier: 135018
modifier: 134982
fast: false
modifier: 135006

145053
stoichiometry: 1.0
species: 536811
type: SpeciesReference

539742
value: 0.3
type: LocalParameter

539402
value: 1.0
type: LocalParameter

168137
stoichiometry: 1.0
species: 536082
type: SpeciesReference

539555
value: 0.3
type: LocalParameter

540268
constant: false
value: 0.0
name: P_UbiqES_S2
type: Parameter

540115
value: 0.119
type: LocalParameter

539969
value: 2.0
type: LocalParameter

149204
stoichiometry: 1.0
species: 536811
type: SpeciesReference

538941
value: 1.0
type: LocalParameter

535368
constant: true
boundary condition: true
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: 534968
name: GENE_P_Hox
type: Species

539743
value: 0.3
type: LocalParameter

539630
value: 0.3
type: LocalParameter

146858
stoichiometry: 1.0
species: 536811
type: SpeciesReference

155561
stoichiometry: 1.0
species: 536302
type: SpeciesReference

160042
stoichiometry: 1.0
species: 536811
type: SpeciesReference

540114
value: 2.0
type: LocalParameter

152680
stoichiometry: 1.0
species: 536137
type: SpeciesReference

540267
constant: false
value: 1.0
name: P_UbiqES_S1
type: Parameter

539403
value: 1.0
type: LocalParameter

539556
value: 0.3
type: LocalParameter

539966
value: 0.119
type: LocalParameter

539740
value: 0.3
type: LocalParameter

168557
stoichiometry: 1.0
species: 536707
type: SpeciesReference

167609
stoichiometry: 1.0
species: 536811
type: SpeciesReference

540113
value: 0.119
type: LocalParameter

539557
value: 0.3
type: LocalParameter

540266
constant: false
value: 0.0
name: P_Gcad_S2
type: Parameter

539404
value: 1.0
type: LocalParameter