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BIOMD0000000139 - Hoffmann2002_KnockOut_IkBNFkB_Signaling

 

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Reference Publication
Publication ID: 12424381
Hoffmann A, Levchenko A, Scott ML, Baltimore D.
The IkappaB-NF-kappaB signaling module: temporal control and selective gene activation.
Science 2002 Nov; 298(5596): 1241-1245
Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.  [more]
Model
Original Model: BIOMD0000000139.xml.origin
Submitter: Harish Dharuri
Submission ID: MODEL7157773062
Submission Date: 15 Aug 2007 21:31:03 UTC
Last Modification Date: 05 Jul 2012 14:45:15 UTC
Creation Date: 16 May 2007 13:37:19 UTC
Encoders:  Harish Dharuri
set #1
bqbiol:isPartOf KEGG Pathway mmu04660
Gene Ontology I-kappaB kinase/NF-kappaB signaling
bqbiol:occursIn Taxonomy Mus musculus
Notes

The model corresponds to the knock out model of beta-/-, epsilon -/- and reproduces the upper panel in Fig 2C. In order to reproduce the other knock out models the transcription rate of the species that are not present must be set to zero and the rate of the one that is present must be set as seven times its corresponding value for the wild type model. This is done so as to compensate for the loss of other isoforms. Model was successfully tested on MathSBML.


To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.


To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Model
Publication ID: 12424381 Submission Date: 15 Aug 2007 21:31:03 UTC Last Modification Date: 05 Jul 2012 14:45:15 UTC Creation Date: 16 May 2007 13:37:19 UTC
Mathematical expressions
Reactions
NFkB-IkBalpha complex formation NFkB-IkBbeta complex formation NFkB-IkBeps complex formation NFkB-binary IKK IkBalpha complex formation
IkBalpha degradation NFkB binary IKK IkBbeta complex formation IkBbeta degradation NFkB binary IKK IkBeps complex formation
IkBeps degradation IkBalpha degradation IkBbeta degradation IkBeps degradation
NFkB translocation NFkB-IkBalpha complex formation NFkB-IkBbeta complex formation NFkB-IkBeps complex formation
IkBalpha transcription IkBalpha inducible transcription IkBalpha transcript degradation IkBbeta transcription
IkBbeta transcript degradation IkBeps transcription IkBeps transcript degradation IKK-IkBalpha complex formation
IkBalpha synthesis IkBalpha degradation IkBalpha translocation IKK-IkBbeta complex formation
IkBbeta synthesis IkBbeta degradation IkBbeta translocation IKK-IkBeps complex formation
IkBeps synthesis IkBeps degradation IkBeps translocation IKK-binary IkBalpha NFkB complex formation
IkBalpha_NFkB translocation IKK binary IkBbeta NFkB complex formation IkBbeta_NFkB translocation IKK binary IkBeps NFkB complex formation
IkBeps_NFkB translocation IkBalpha degradation IkBbeta degradation IkBeps degradation
IKK consumption      
Rules
Assignment Rule (variable: Total_IkBbeta) Assignment Rule (variable: Total_IkBeps) Assignment Rule (variable: Total_IkBalpha) Assignment Rule (variable: Total_NFkBn)
Rate Rule (variable: fr_after_trigger)      
Events
event_0000001      
Physical entities
Compartments Species
cytoplasm IkBalpha NFkB IkBalpha_NFkB
IkBbeta IkBbeta_NFkB IkBeps
IkBeps_NFkB IKK_IkBalpha IKK_IkBalpha_NFkB
IKK IKK_IkBbeta IKK_IkBbeta_NFkB
IKK_IkBeps IKK_IkBeps_NFkB  
nucleus NFkB_nuc IkBalpha_nuc IkBalpha_nuc_NFkB_nuc
IkBbeta_nuc IkBbeta_nuc_NFkB_nuc IkBeps_nuc
IkBalpha_transcript IkBbeta_transcript IkBeps_transcript
IkBeps_nuc_NFkB_nuc    
Global parameters
a4 d4 a5 d5
a6 d6 r4 r5
r6 deg4 k1 k01
tr2a tr2 tr3 tr2b
tr2e a1 d1 tr1
deg1 tp1 tp2 a2
d2 a3 d3 a7
k2 a8 k2_beta a9
k2_eps r1 r2 r3
k02 trigger_value fr fr_after_trigger
Total_IkBbeta Total_IkBeps Total_IkBalpha Total_NFkBn
flag_for_after_trigger      
Reactions (45)
 
 NFkB-IkBalpha complex formation [NFkB] + [IkBalpha] ↔ [IkBalpha_NFkB];  
 
 NFkB-IkBbeta complex formation [NFkB] + [IkBbeta] ↔ [IkBbeta_NFkB];  
 
 NFkB-IkBeps complex formation [NFkB] + [IkBeps] ↔ [IkBeps_NFkB];  
 
 NFkB-binary IKK IkBalpha complex formation [NFkB] + [IKK_IkBalpha] ↔ [IKK_IkBalpha_NFkB];  
 
 IkBalpha degradation [IKK_IkBalpha_NFkB] → [NFkB] + [IKK];  
 
 NFkB binary IKK IkBbeta complex formation [NFkB] + [IKK_IkBbeta] ↔ [IKK_IkBbeta_NFkB];  
 
 IkBbeta degradation [IKK_IkBbeta_NFkB] → [NFkB] + [IKK];  
 
 NFkB binary IKK IkBeps complex formation [NFkB] + [IKK_IkBeps] ↔ [IKK_IkBeps_NFkB];  
 
 IkBeps degradation [IKK_IkBeps_NFkB] → [NFkB] + [IKK];  
 
 IkBalpha degradation [IkBalpha_NFkB] → [NFkB];  
 
 IkBbeta degradation [IkBbeta_NFkB] → [NFkB];  
 
 IkBeps degradation [IkBeps_NFkB] → [NFkB];  
 
 NFkB translocation [NFkB] ↔ [NFkB_nuc];  
 
 NFkB-IkBalpha complex formation [NFkB_nuc] + [IkBalpha_nuc] ↔ [IkBalpha_nuc_NFkB_nuc];  
 
 NFkB-IkBbeta complex formation [NFkB_nuc] + [IkBbeta_nuc] ↔ [IkBbeta_nuc_NFkB_nuc];  
 
 NFkB-IkBeps complex formation [NFkB_nuc] + [IkBeps_nuc] ↔ [IkBeps_nuc_NFkB_nuc];  
 
 IkBalpha transcription  → [IkBalpha_transcript];  
 
 IkBalpha inducible transcription  → [IkBalpha_transcript];   {NFkB_nuc}
 
 IkBalpha transcript degradation [IkBalpha_transcript] → ;  
 
 IkBbeta transcription  → [IkBbeta_transcript];  
 
 IkBbeta transcript degradation [IkBbeta_transcript] → ;  
 
 IkBeps transcription  → [IkBeps_transcript];  
 
 IkBeps transcript degradation [IkBeps_transcript] → ;  
 
 IKK-IkBalpha complex formation [IKK] + [IkBalpha] ↔ [IKK_IkBalpha];  
 
 IkBalpha synthesis  → [IkBalpha];   {IkBalpha_transcript}
 
 IkBalpha degradation [IkBalpha] → ;  
 
 IkBalpha translocation [IkBalpha] ↔ [IkBalpha_nuc];  
 
 IKK-IkBbeta complex formation [IKK] + [IkBbeta] ↔ [IKK_IkBbeta];  
 
 IkBbeta synthesis  → [IkBbeta];   {IkBbeta_transcript}
 
 IkBbeta degradation [IkBbeta] → ;  
 
 IkBbeta translocation [IkBbeta] ↔ [IkBbeta_nuc];  
 
 IKK-IkBeps complex formation [IKK] + [IkBeps] ↔ [IKK_IkBeps];  
 
 IkBeps synthesis  → [IkBeps];   {IkBeps_transcript}
 
 IkBeps degradation [IkBeps] → ;  
 
 IkBeps translocation [IkBeps] ↔ [IkBeps_nuc];  
 
 IKK-binary IkBalpha NFkB complex formation [IKK] + [IkBalpha_NFkB] ↔ [IKK_IkBalpha_NFkB];  
 
 IkBalpha_NFkB translocation [IkBalpha_nuc_NFkB_nuc] → [IkBalpha_NFkB];  
 
 IKK binary IkBbeta NFkB complex formation [IKK] + [IkBbeta_NFkB] ↔ [IKK_IkBbeta_NFkB];  
 
 IkBbeta_NFkB translocation [IkBbeta_nuc_NFkB_nuc] → [IkBbeta_NFkB];  
 
 IKK binary IkBeps NFkB complex formation [IKK] + [IkBeps_NFkB] ↔ [IKK_IkBeps_NFkB];  
 
 IkBeps_NFkB translocation [IkBeps_nuc_NFkB_nuc] → [IkBeps_NFkB];  
 
 IkBalpha degradation [IKK_IkBalpha] → [IKK];  
 
 IkBbeta degradation [IKK_IkBbeta] → [IKK];  
 
 IkBeps degradation [IKK_IkBeps] → [IKK];  
 
 IKK consumption [IKK] → ;  
 
Rules (5)
 
 Assignment Rule (name: Total_IkBbeta) Total_IkBbeta = IkBbeta+IkBbeta_NFkB+IKK_IkBbeta+IKK_IkBbeta_NFkB
 
 Assignment Rule (name: Total_IkBeps) Total_IkBeps = IkBeps+IkBeps_NFkB+IKK_IkBeps+IKK_IkBeps_NFkB
 
 Assignment Rule (name: Total_IkBalpha) Total_IkBalpha = IkBalpha+IkBalpha_NFkB+IKK_IkBalpha+IKK_IkBalpha_NFkB
 
 Assignment Rule (name: Total_NFkBn) Total_NFkBn = IkBbeta_nuc_NFkB_nuc+NFkB_nuc
 
 Rate Rule (name: fr_after_trigger) d [ fr_after_trigger] / d t= trigger_value*(-0.5)/(1+(t-2000))^2
 
Events (1)
 
 event_0000001
IKK = 0.1
trigger_value = 1
flag_for_after_trigger = 0
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 IkBalpha
Compartment: cytoplasm
Initial concentration: 0.1
 
 NFkB
Compartment: cytoplasm
Initial concentration: 0.1
 
 IkBalpha_NFkB
Compartment: cytoplasm
Initial concentration: 0.0
 
 IkBbeta
Compartment: cytoplasm
Initial concentration: 0.0
 
 IkBbeta_NFkB
Compartment: cytoplasm
Initial concentration: 0.0
 
 IkBeps
Compartment: cytoplasm
Initial concentration: 0.0
 
 IkBeps_NFkB
Compartment: cytoplasm
Initial concentration: 0.0
 
 IKK_IkBalpha
Compartment: cytoplasm
Initial concentration: 0.0
 
 IKK_IkBalpha_NFkB
Compartment: cytoplasm
Initial concentration: 0.0
 
 IKK
Compartment: cytoplasm
Initial concentration: 0.0
 
 IKK_IkBbeta
Compartment: cytoplasm
Initial concentration: 0.0
 
 IKK_IkBbeta_NFkB
Compartment: cytoplasm
Initial concentration: 0.0
 
 IKK_IkBeps
Compartment: cytoplasm
Initial concentration: 0.0
 
 IKK_IkBeps_NFkB
Compartment: cytoplasm
Initial concentration: 0.0
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 NFkB_nuc
Compartment: nucleus
Initial concentration: 0.0010
 
 IkBalpha_nuc
Compartment: nucleus
Initial concentration: 0.0
 
 IkBalpha_nuc_NFkB_nuc
Compartment: nucleus
Initial concentration: 0.0
 
 IkBbeta_nuc
Compartment: nucleus
Initial concentration: 0.0
 
 IkBbeta_nuc_NFkB_nuc
Compartment: nucleus
Initial concentration: 0.0
 
 IkBeps_nuc
Compartment: nucleus
Initial concentration: 0.0
 
   IkBalpha_transcript
Compartment: nucleus
Initial concentration: 0.0
 
   IkBbeta_transcript
Compartment: nucleus
Initial concentration: 0.0
 
   IkBeps_transcript
Compartment: nucleus
Initial concentration: 0.0
 
 IkBeps_nuc_NFkB_nuc
Compartment: nucleus
Initial concentration: 0.0
 
Global Parameters (45)
 
   a4
Value: 30.0
Constant
 
   d4
Value: 0.03
Constant
 
   a5
Value: 30.0
Constant
 
   d5
Value: 0.03
Constant
 
   a6
Value: 30.0
Constant
 
   d6
Value: 0.03
Constant
 
   r4
Value: 1.224
Constant
 
   r5
Value: 0.45
Constant
 
   r6
Value: 0.66
Constant
 
   deg4
Value: 0.00135
Constant
 
   k1
Value: 5.4
Constant
 
   k01
Value: 0.0048
Constant
 
   tr2a
Value: 9.25E-5
Constant
 
   tr2
Value: 0.99
Constant
 
   tr3
Value: 0.0168
Constant
 
   tr2b
Constant
 
   tr2e
Constant
 
   a1
Value: 1.35
Constant
 
   d1
Value: 0.075
Constant
 
   tr1
Value: 0.2448
Constant
 
   deg1
Value: 0.00678
Constant
 
   tp1
Value: 0.018
Constant
 
   tp2
Value: 0.012
Constant
 
   a2
Value: 0.36
Constant
 
   d2
Value: 0.105
Constant
 
   a3
Value: 0.54
Constant
 
   d3
Value: 0.105
Constant
 
   a7
Value: 11.1
Constant
 
   k2
Value: 0.828
Constant
 
   a8
Value: 2.88
Constant
 
   k2_beta
Value: 0.624
Constant
 
   a9
Value: 4.2
Constant
 
   k2_eps
Value: 0.624
Constant
 
   r1
Value: 0.2442
Constant
 
   r2
Value: 0.09
Constant
 
   r3
Value: 0.132
Constant
 
   k02
Value: 0.0072
Constant
 
   trigger_value  
 
   fr
Value: 1.0
 
   fr_after_trigger
Value: 0.5
 
   Total_IkBbeta
Value: NaN
 
   Total_IkBeps
Value: NaN
 
   Total_IkBalpha
Value: NaN
 
   Total_NFkBn
Value: NaN
 
   flag_for_after_trigger
Value: 0.5
 
IkBbeta_NFkB translocation (1)
 
   k2_IkBbeta_nuc_NFkB_nuc
Value: 0.0069
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000139

Curator's comment: (updated: 15 Aug 2007 07:11:26 BST)

Plot corresponds to the upper panel of Fig 2C of the paper. Simulation result obtained from MathSBML.

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