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BIOMD0000000596 - Philipson2015 - Innate immune response modulated by NLRX1

 

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Reference Publication
Publication ID: 26367386
Philipson CW, Bassaganya-Riera J, Viladomiu M, Kronsteiner B, Abedi V, Hoops S, Michalak P, Kang L, Girardin SE, Hontecillas R.
Modeling the Regulatory Mechanisms by Which NLRX1 Modulates Innate Immune Responses to Helicobacter pylori Infection.
PLoS ONE 2015; 10(9): e0137839
Center for Modeling Immunity to Enteric Pathogens, Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, VA, United States of America; Nutritional Immunology and Molecular Medicine Laboratory, Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, VA, United States of America.  [more]
Model
Original Model: BIOMD0000000596.origin
Submitter: Casandra Philipson
Submission ID: MODEL1508180000
Submission Date: 18 Aug 2015 18:01:04 UTC
Last Modification Date: 30 Mar 2016 16:13:34 UTC
Creation Date: 25 Sep 2014 15:31:14 UTC
Encoders:  Vijayalakshmi Chelliah
   Casandra Philipson
set #1
bqbiol:hasTaxon Taxonomy Mus musculus
Taxonomy Helicobacter pylori
set #2
bqbiol:isVersionOf Gene Ontology symbiosis, encompassing mutualism through parasitism
Gene Ontology response to bacterium
Gene Ontology innate immune response
set #3
bqbiol:occursIn Brenda Tissue Ontology BTO:0000141
set #4
bqbiol:hasProperty Human Disease Ontology DOID:3686
Notes
Model
Publication ID: 26367386 Submission Date: 18 Aug 2015 18:01:04 UTC Last Modification Date: 30 Mar 2016 16:13:34 UTC Creation Date: 25 Sep 2014 15:31:14 UTC
Mathematical expressions
Reactions
MyD88_a_HP MyD88_d TRAF_d NFkB_a1
NFkB_d CytoL_a CytoL_d NLRX1_d
MyD88_a HP_a HP_CytoL NLRX1_TF
NFkB_a2 RIG_a_HP RIG_d MAVS_a
MAVS_d IRF_a1 IRF_a2 IRF_a3
IRF_d IFN_a IFN_d NOD_a
NOD_d HP_IFN TRAF_a TFa_a
TFa_d TFi_a TFi_d CytoE_a
CytoE_d X_a X_d HP_CytoE
Physical entities
Compartments Species
default HP NLRX1 CytoL
MyD88 TRAF6 NFkB
IFN NOD1 RIG
MAVS IRF TFa
CytoE TFi X
Global parameters
n      
Reactions (36)
 
 MyD88_a_HP  → [MyD88];   {HP} , {HP} , {HP}
 
 MyD88_d [MyD88] → ;   {MyD88} , {MyD88}
 
 TRAF_d [TRAF6] → ;   {TRAF6} , {TRAF6}
 
 NFkB_a1  → [NFkB];   {NLRX1} , {TRAF6} , {NLRX1} , {TRAF6} , {NLRX1} , {TRAF6}
 
 NFkB_d [NFkB] → ;   {NFkB} , {NFkB}
 
 CytoL_a  → [CytoL];   {NFkB} , {NFkB} , {NFkB}
 
 CytoL_d [CytoL] → ;   {CytoL} , {CytoL}
 
 NLRX1_d [NLRX1] → ;   {NLRX1} , {NLRX1}
 
 MyD88_a  → [MyD88];   {CytoL} , {CytoL} , {CytoL}
 
 HP_a  → [HP];   {HP} , {HP}
 
 HP_CytoL [HP] → ;   {CytoL} , {CytoL} , {CytoL}
 
 NLRX1_TF  → [NLRX1];   {TFi} , {TFa} , {TFi} , {TFa} , {TFi} , {TFa}
 
 NFkB_a2  → [NFkB];   {NOD1} , {NOD1} , {NOD1}
 
 RIG_a_HP  → [RIG];   {HP} , {HP} , {HP}
 
 RIG_d [RIG] → ;   {RIG} , {RIG}
 
 MAVS_a  → [MAVS];   {NLRX1} , {RIG} , {NLRX1} , {RIG} , {NLRX1} , {RIG}
 
 MAVS_d [MAVS] → ;   {MAVS} , {MAVS}
 
 IRF_a1  → [IRF];   {MAVS} , {MAVS} , {MAVS}
 
 IRF_a2  → [IRF];   {NOD1} , {NOD1} , {NOD1}
 
 IRF_a3  → [IRF];   {IFN} , {IFN} , {IFN}
 
 IRF_d [IRF] → ;   {IRF} , {IRF}
 
 IFN_a  → [IFN];   {IRF} , {IRF} , {IRF}
 
 IFN_d [IFN] → ;   {IFN} , {IFN}
 
 NOD_a  → [NOD1];   {HP} , {HP} , {HP}
 
 NOD_d [NOD1] → ;   {NOD1} , {NOD1}
 
 HP_IFN [HP] → ;   {IFN} , {IFN} , {IFN}
 
 TRAF_a  → [TRAF6];   {X} , {MyD88} , {X} , {MyD88} , {X} , {MyD88}
 
 TFa_a  → [TFa];   {CytoL} , {CytoL} , {CytoL}
 
 TFa_d [TFa] → ;   {TFa} , {TFa}
 
 TFi_a  → [TFi];   {CytoE} , {CytoE} , {CytoE}
 
 TFi_d [TFi] → ;   {TFi} , {TFi}
 
 CytoE_a  → [CytoE];   {X} , {NFkB} , {X} , {NFkB} , {X} , {NFkB}
 
 CytoE_d [CytoE] → ;   {CytoE} , {CytoE}
 
 X_a  → [X];   {NFkB} , {NFkB} , {NFkB}
 
 X_d [X] → ;   {X} , {X}
 
 HP_CytoE [HP] → ;   {CytoE} , {CytoE} , {CytoE}
 
Functions (4)
 
 CWP Logistic lambda(k, r, s, r*s*(1-s/k))
 
 CWP hill lambda(vmax, s, shalve, n, vmax*s^n/(shalve^n+s^n))
 
 CWP Hill Inhibitor lambda(n, i, ki, ka, a, ka*a*1/(1+(i/ki)^n))
 
 1/2 MA lambda(k, A, k*A/2)
 
 default Spatial dimensions: 3.0  Compartment size: 1.0
 
 HP
Compartment: default
Initial concentration: 4.4
 
 NLRX1
Compartment: default
Initial concentration: 0.9
 
 CytoL
Compartment: default
Initial concentration: 1.0
 
 MyD88
Compartment: default
Initial concentration: 0.9
 
 TRAF6
Compartment: default
Initial concentration: 0.9
 
 NFkB
Compartment: default
Initial concentration: 0.9
 
 IFN
Compartment: default
Initial concentration: 1.0
 
 NOD1
Compartment: default
Initial concentration: 0.9
 
 RIG
Compartment: default
Initial concentration: 0.9
 
 MAVS
Compartment: default
Initial concentration: 0.6
 
 IRF
Compartment: default
Initial concentration: 1.0
 
 TFa
Compartment: default
Initial concentration: 1.0
 
 CytoE
Compartment: default
Initial concentration: 1.0
 
 TFi
Compartment: default
Initial concentration: 1.0
 
 X
Compartment: default
Initial concentration: 1.0
 
Global Parameters (1)
 
 n
Value: 1.0
Constant
 
MyD88_a_HP (2)
 
   vmax
Value: 0.00211822327180341
Constant
 
   shalve
Value: 0.00167453984032407
Constant
 
MyD88_d (1)
 
   k1
Value: 0.00123453
Constant
 
TRAF_d (1)
 
   k1
Value: 0.0103771276
Constant
 
NFkB_a1 (2)
 
   ki
Value: 0.04779118
Constant
 
   ka
Value: 1.1676376672
Constant
 
NFkB_d (1)
 
   k1
Value: 0.07507042903
Constant
 
CytoL_a (2)
 
   vmax
Value: 0.096005
Constant
 
   shalve
Value: 0.00405
Constant
 
CytoL_d (1)
 
   k1
Value: 0.00608
Constant
 
NLRX1_d (1)
 
   k1
Value: 0.00593
Constant
 
MyD88_a (2)
 
   vmax
Value: 0.00283798482417334
Constant
 
   shalve
Value: 0.00154976502305966
Constant
 
HP_a (2)
 
   k
Value: 6.47754122346905
Constant
 
   r
Value: 0.0231262309
Constant
 
HP_CytoL (1)
 
   k
Value: 0.00457696687976
Constant
 
NLRX1_TF (2)
 
   ki
Value: 0.008882000955
Constant
 
   ka
Value: 0.42313
Constant
 
NFkB_a2 (2)
 
   vmax
Value: 0.6347384122
Constant
 
   shalve
Value: 1.8846156538
Constant
 
RIG_a_HP (2)
 
   vmax
Value: 0.0118173887503611
Constant
 
   shalve
Value: 0.00143140224694888
Constant
 
RIG_d (1)
 
   k1
Value: 0.0010377234048545
Constant
 
MAVS_a (2)
 
   ki
Value: 0.033496867888
Constant
 
   ka
Value: 0.007477722639
Constant
 
MAVS_d (1)
 
   k1
Value: 0.001592
Constant
 
IRF_a1 (2)
 
   vmax
Value: 0.0062174
Constant
 
   shalve
Value: 1.44358
Constant
 
IRF_a2 (2)
 
   vmax
Value: 0.0980062665
Constant
 
   shalve
Value: 9.64990135143775
Constant
 
IRF_a3 (2)
 
   vmax
Value: 0.30137407572
Constant
 
   shalve
Value: 44.7674128755764
Constant
 
IRF_d (1)
 
   k1
Value: 0.004789221404
Constant
 
IFN_a (2)
 
   vmax
Value: 0.4898378115082
Constant
 
   shalve
Value: 49.92877782
Constant
 
IFN_d (1)
 
   k1
Value: 0.00523855748474113
Constant
 
NOD_a (2)
 
   vmax
Value: 0.006623396018441
Constant
 
   shalve
Value: 0.00178530769571592
Constant
 
NOD_d (1)
 
   k1
Value: 0.00122637229001114
Constant
 
HP_IFN (1)
 
   k
Value: 1.0E-5
Constant
 
TRAF_a (2)
 
   ki
Value: 0.08812845453
Constant
 
   ka
Value: 0.739178470625
Constant
 
TFa_a (2)
 
   vmax
Value: 0.0205163346419065
Constant
 
   shalve
Value: 0.79845410165576
Constant
 
TFa_d (1)
 
   k1
Value: 0.00830409028
Constant
 
TFi_a (2)
 
   vmax
Value: 0.0902778190945806
Constant
 
   shalve
Value: 3.083541152
Constant
 
TFi_d (1)
 
   k1
Value: 0.0324619644365822
Constant
 
CytoE_a (2)
 
   ki
Value: 0.04806833192
Constant
 
   ka
Value: 12.20282
Constant
 
CytoE_d (1)
 
   k1
Value: 0.03676294
Constant
 
X_a (2)
 
   vmax
Value: 0.046393325
Constant
 
   shalve
Value: 0.003976
Constant
 
X_d (1)
 
   k1
Value: 0.002227925238504
Constant
 
HP_CytoE (1)
 
   k
Value: 1.5E-4
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000596

Curator's comment: (updated: 30 Mar 2016 15:46:22 GMT)

The model reproduces the wildtype condition, i.e. figure 3E of the reference publication. The model is not opening in any other tools (tried with CellDesigner, SimBiology, DEDiscover, SBMLodeSolver) except for Copasi as it has SBML layout package. So, the simulation result has been tested using Copasi v4.16 (Build 104)(the paper has also used Copasi for simulation).

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