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Pathway List for mapk

Default ordering is done according to Pathway Name.Table header can be used for changing the default ordering.
indicates that ordering is done according to ascending or descending order.
Entries are color tagged depending on Network  or Pathway 
  Pathway Name
Pathway No.
Accession Name
Accession No.
Accession
Type
Pathway statisticsmapk statisticsSource
Entry Date
1 MAPK
Pathway No. 6
 fig2_egfr

Accession No. 1
NetworkMolecule = 9
Enzyme   = 4
Reaction  = 0
Molecule = 1
Enzyme   = 0
Reaction  = 0
Bhalla US and Iyengar R. Science (1999) 283(5400):381-7. ( peer-reviewed publication )/
2001-11-07
   Related Pathway: 
2435566175139142182193211230317335352366371377384390396402403409415
421432438444450456462468474480486492498504510516522528535541547553559565
571577583589595601607613619625631637643649655661667673679686692699704710
716722728734740746752758764770776782788794800806812818824830836842848854
860866872878884890896902908914921928934940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    This network was used to generate figure 2 in Bhalla US and Iyengar R. Science (1999) 283(5400):381-7. It consists of the MAPK cascade in a feedback loop with PKC, and receives input from the EGFR in the synapse.
Demonstration script files for generating the figures in the paper, including figure 2, are available here.
   
This pathway is part of accession 1 and is completely specified in the file acc1.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc1.g   
GENESIS Format (Annotated version)    Anno_acc1.g   
2 MAPK
Pathway No. 24
 fig4_synapse

Accession No. 3
NetworkMolecule = 9
Enzyme   = 4
Reaction  = 0
Molecule = 1
Enzyme   = 0
Reaction  = 0
Bhalla US and Iyengar R. Science (1999) 283(5400):381-7. ( peer-reviewed publication )/
2001-11-07
   Related Pathway: 
635566175139142182193211230317335352366371377384390396402403409415421
432438444450456462468474480486492498504510516522528535541547553559565571
577583589595601607613619625631637643649655661667673679686692699704710716
722728734740746752758764770776782788794800806812818824830836842848854860
866872878884890896902908914921928934940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    This is the composite model of 4 kinases: PKC, MAPK, PKA and CaMKII and numerous regulatory pathways involved in synaptic signaling. From Bhalla US and Iyengar R. Science (1999) 283(5400):381-7.This model comes from figure 4 of that paper.
Demonstration script files for generating the figures in the paper, including figure 4, are available here.
   
This pathway is part of accession 3 and is completely specified in the file acc3.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc3.g   
GENESIS Format (Annotated version)    Anno_acc3.g   
3 MAPK
Pathway No. 35
 mkp1_feedback_
effects

Accession No. 4
NetworkMolecule = 16
Enzyme   = 9
Reaction  = 8
Molecule = 1
Enzyme   = 0
Reaction  = 0
Bhalla US et al. Science (2002) 297(5583):1018-23. ( peer-reviewed publication )/
2001-11-07
   Related Pathway: 
624566175139142182193211230317335352366371377384390396402403409415421
432438444450456462468474480486492498504510516522528535541547553559565571
577583589595601607613619625631637643649655661667673679686692699704710716
722728734740746752758764770776782788794800806812818824830836842848854860
866872878884890896902908914921928934940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    The Mitogen Activated Protein Kinase (MAPK) cascade model here includes both the MAPK cascade and its regulation by two forms of MKP. MKP-1 is induced upon MAPK activation, whereas MKP-2 is treated as a steady level of protein. The phosphatase Protein phosphatase 2 A (PP2A) is also included in this model to balance the activity of the kinases.
   
This pathway is part of accession 4 and is completely specified in the file acc4.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc4.g   
GENESIS Format (Annotated version)    Anno_acc4.g   
MATLAB format    acc4.m   
SBML format    acc4.xml   
4 MAPK
Pathway No. 56
 3d_fold_model

Accession No. 8
NetworkMolecule = 9
Enzyme   = 4
Reaction  = 0
Molecule = 1
Enzyme   = 0
Reaction  = 0
Bhalla US and Iyengar R. Science (1999) 283(5400):381-7. ( peer-reviewed publication )/
2001-11-08
   Related Pathway: 
624356175139142182193211230317335352366371377384390396402403409415421
432438444450456462468474480486492498504510516522528535541547553559565571
577583589595601607613619625631637643649655661667673679686692699704710716
722728734740746752758764770776782788794800806812818824830836842848854860
866872878884890896902908914921928934940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    This model is an annotated version of the synaptic signaling network.
The primary reference is Bhalla US and Iyengar R. Science (1999) 283(5400):381-7 but several of the model pathways have been updated Bhalla US, Ram PT, Iyengar R. Science. 2002 Aug 9;297(5583):1018-23.
   
This pathway is part of accession 8 and is completely specified in the file acc8.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc8.g   
GENESIS Format (Annotated version)    Anno_acc8.g   
MATLAB format    acc8.m   
SBML format    acc8.xml   
5 MAPK
Pathway No. 61
 MAPK_MKP1_
oscillation

Accession No. 9
NetworkMolecule = 15
Enzyme   = 9
Reaction  = 7
Molecule = 1
Enzyme   = 0
Reaction  = 0
Bhalla US, Iyengar R. Chaos (2001) 11(1):221-226. ( peer-reviewed publication )/
2001-11-08
   Related Pathway: 
624355675139142182193211230317335352366371377384390396402403409415421
432438444450456462468474480486492498504510516522528535541547553559565571
577583589595601607613619625631637643649655661667673679686692699704710716
722728734740746752758764770776782788794800806812818824830836842848854860
866872878884890896902908914921928934940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    This model relates to figure 5 in Bhalla US, Iyengar R. Chaos (2001) 11(1):221-226. It includes the model used for figures 2-4 and also has MKP-1 induction by MAPK activity in the synapse. PP2A is set to 0.16 uM and MKP synthesis is varied from 5x to 40 x basal to get a range of interesting behaviours.
   
This pathway is part of accession 9 and is completely specified in the file acc9.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc9.g   
GENESIS Format (Annotated version)    Anno_acc9.g   
GENESIS Format (Annotated version)    Anno_acc9.g   
MATLAB format    acc9.m   
SBML format    acc9.xml   
6 MAPK
Pathway No. 75
 Synaptic_
Network

Accession No. 16
NetworkMolecule = 9
Enzyme   = 4
Reaction  = 0
Molecule = 1
Enzyme   = 0
Reaction  = 0
Bhalla US and Iyengar R. Science (1999) 283(5400):381-7. ( peer-reviewed publication )/
2001-12-12
   Related Pathway: 
624355661139142182193211230317335352366371377384390396402403409415421
432438444450456462468474480486492498504510516522528535541547553559565571
577583589595601607613619625631637643649655661667673679686692699704710716
722728734740746752758764770776782788794800806812818824830836842848854860
866872878884890896902908914921928934940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    The Mitogen Activated Protein Kinase (MAPK) cascade model here includes both the MAPK cascade and its regulation by MKP-1. MKP-1 is induced upon MAPK activation, whereas MKP-2 is treated as a steady level of protein. For the purposes of this version of the model, MKP-1 is kept at a fixed starting value. The phosphatase Protein phosphatase 2 A (PP2A) is also included in this model to balance the activity of the kinases.
   
This pathway is part of accession 16 and is completely specified in the file acc16.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc16.g   
GENESIS Format (Annotated version)    Anno_acc16.g   
7 MAPK
Pathway No. 139
 MAPK_osc

Accession No. 27
PathwayMolecule = 15
Enzyme   = 10
Reaction  = 1
Molecule = 1
Enzyme   = 0
Reaction  = 0
Boris N. Kholodenko Eur J Biochem. (2000) 267(6):1583-8). ( peer-reviewed publication )/
2002-01-22
   Related Pathway: 
62435566175142182193211230317335352366371377384390396402403409415421
432438444450456462468474480486492498504510516522528535541547553559565571
577583589595601607613619625631637643649655661667673679686692699704710716
722728734740746752758764770776782788794800806812818824830836842848854860
866872878884890896902908914921928934940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    This is the oscillatory MAPK model from Kholodenko 2000 Eur J. Biochem 267:1583-1588 The original model is formulated in terms of idealized Michaelis-Menten enzymes and the enzyme-substrate complex concentrations are therefore assumed negligible. The current implementation of the model uses explicit enzyme reactions involving substrates and is therefore an approximation to the Kholodenko model. The approximation is greatly improved if the enzyme is flagged as Available which is an option in Kinetikit. This flag means that the enzyme protein concentration is not reduced even when it is involved in a complex. However, the substrate protein continues to participate in enzyme-substrate complexes and its concentration is therefore affected. Overall, this model works almost the same as the Kholodenko model but the peak MAPK-PP amplitudes are a little reduced and the period of oscillations is about 10% longer. If the enzymes are not flagged as Available then the oscillations commence only when the Km for enzyme 1 is set to 0.1 uM.
   
This pathway is part of accession 27 and is completely specified in the file acc27.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc27.g   
GENESIS Format (Annotated version)    Anno_acc27.g   
MATLAB format    acc27.m   
SBML format    acc27.xml   
8 MAPK
Pathway No. 142
 Huang_Ferrell_
MAPK

Accession No. 30
PathwayMolecule = 14
Enzyme   = 10
Reaction  = 0
Molecule = 1
Enzyme   = 0
Reaction  = 0
Huang CY and Ferrell JE Jr. Proc Natl Acad Sci U S A. (1996) 93(19):10078-83 ( peer-reviewed publication )/
2002-01-31
   Related Pathway: 
62435566175139182193211230317335352366371377384390396402403409415421
432438444450456462468474480486492498504510516522528535541547553559565571
577583589595601607613619625631637643649655661667673679686692699704710716
722728734740746752758764770776782788794800806812818824830836842848854860
866872878884890896902908914921928934940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    MAPK model by Huang, C.-Y.F. and Ferrell Jr., J.E. 1996 PNAS USA 93:10078-10083 The parameters are based on the Mathematica code for the model which was kindly supplied by Prof. Ferrell. This simulation very closely replicates figure 2 from the paper.
   
This pathway is part of accession 30 and is completely specified in the file acc30.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc30.g   
GENESIS Format (Annotated version)    Anno_acc30.g   
MATLAB format    acc30.m   
SBML format    acc30.xml   
9 MAPK
Pathway No. 182
 MAPK-bistability
-fig1c

Accession No. 35
NetworkMolecule = 10
Enzyme   = 6
Reaction  = 0
Molecule = 1
Enzyme   = 0
Reaction  = 0
Bhalla US et al. Science (2002) 297(5583):1018-23 ( peer-reviewed publication )./
2002-11-07
   Related Pathway: 
62435566175139142193211230317335352366371377384390396402403409415421
432438444450456462468474480486492498504510516522528535541547553559565571
577583589595601607613619625631637643649655661667673679686692699704710716
722728734740746752758764770776782788794800806812818824830836842848854860
866872878884890896902908914921928934940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    The Mitogen Activated Protein Kinase (MAPK) cascade model here includes both the MAPK cascade and its regulation by two forms of MKP. MKP-1 is induced upon MAPK activation, whereas MKP-2 is treated as a steady level of protein. The phosphatase Protein phosphatase 2 A (PP2A) is also included in this model to balance the activity of the kinases.
   
This pathway is part of accession 35 and is completely specified in the file acc35.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc35.g   
GENESIS Format (Annotated version)    Anno_acc35.g   
MATLAB format    acc35.m   
SBML format    acc35.xml   
10 MAPK
Pathway No. 193
 MAPK_Asthagiri_
adapt_fb

Accession No. 45
PathwayMolecule = 26
Enzyme   = 11
Reaction  = 7
Molecule = 0
Enzyme   = 0
Reaction  = 0
Asthagiri AR and Lauffenburger DA. Biotechnol Prog. (2001) 17(2):227-39. ( peer-reviewed publication )./
2003-02-22
   Related Pathway: 
62435566175139142182211230317335352366371377384390396402403409415421
432438444450456462468474480486492498504510516522528535541547553559565571
577583589595601607613619625631637643649655661667673679686692699704710716
722728734740746752758764770776782788794800806812818824830836842848854860
866872878884890896902908914921928934940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    This is a complex model to examine mechanisms that govern MAPK pathway dynamics in Chinese hamster ovary (CHO) cell lines, particularly the role of adapter targeted negative feedback mechanism in generating complete signal adaptation. This model simulates the results as per the figure 7A of the paper by Asthagiri AR and Lauffenburger DA. Biotechnol Prog. (2001) 17(2):227-39.
   
This pathway is part of accession 45 and is completely specified in the file acc45.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc45.g   
GENESIS Format (Annotated version)    Anno_acc45.g   
MATLAB format    acc45.m   
SBML format    acc45.xml   
11 MAPK
Pathway No. 211
 MAPK_network_
2003

Accession No. 50
NetworkMolecule = 9
Enzyme   = 4
Reaction  = 0
Molecule = 1
Enzyme   = 0
Reaction  = 0
Bhalla US Biophys J. 2004 Aug;87(2):745-53. ( peer-reviewed publication )/
2003-04-28
   Related Pathway: 
62435566175139142182193230317335352366371377384390396402403409415421
432438444450456462468474480486492498504510516522528535541547553559565571
577583589595601607613619625631637643649655661667673679686692699704710716
722728734740746752758764770776782788794800806812818824830836842848854860
866872878884890896902908914921928934940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    This is a network model of many pathways present at the neuronal synapse. The network has properties of temporal tuning as well as steady-state computational properties. In its default form the network is bistable.Bhalla US Biophys J. 2004 Aug;87(2):745-53
   
This pathway is part of accession 50 and is completely specified in the file acc50.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc50.g   
GENESIS Format (Annotated version)    Anno_acc50.g   
MATLAB format    acc50.m   
SBML format    acc50.xml   
12 MAPK
Pathway No. 230
 EGFR_MAPK

Accession No. 58
NetworkMolecule = 9
Enzyme   = 4
Reaction  = 0
Molecule = 1
Enzyme   = 0
Reaction  = 0
Bhalla US. Biophys J. (2004) 87(2):745-53. ( peer-reviewed publication )/
2004-01-14
   Related Pathway: 
62435566175139142182193211317335352366371377384390396402403409415421
432438444450456462468474480486492498504510516522528535541547553559565571
577583589595601607613619625631637643649655661667673679686692699704710716
722728734740746752758764770776782788794800806812818824830836842848854860
866872878884890896902908914921928934940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    Model of MAPK activation by EGFR in the synapse. Demonstration programs using this model are available here.
Primary citation:Bhalla US. Biophys J. (2004) 87(2):745-53.
   
This pathway is part of accession 58 and is completely specified in the file acc58.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc58.g   
GENESIS Format (Annotated version)    Anno_acc58.g   
MATLAB format    acc58.m   
SBML format    acc58.xml   
13 MAPK
Pathway No. 317
 Ajay_Bhalla_
2004_PKM_Tuning

Accession No. 76
NetworkMolecule = 10
Enzyme   = 6
Reaction  = 0
Molecule = 1
Enzyme   = 0
Reaction  = 0
Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80. ( Peer-reviewed publication )/
2006-12-12
   Related Pathway: 
62435566175139142182193211230335352366371377384390396402403409415421
432438444450456462468474480486492498504510516522528535541547553559565571
577583589595601607613619625631637643649655661667673679686692699704710716
722728734740746752758764770776782788794800806812818824830836842848854860
866872878884890896902908914921928934940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    This model is taken from the Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80. This is the reference feedforward model from Figure 8a.
   
This pathway is part of accession 76 and is completely specified in the file acc76.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc76.g   
MATLAB format    acc76.m   
SBML format    acc76.xml   
14 MAPK
Pathway No. 335
 Ajay_Bhalla_
2004_PKM_MKP3_
Tuning

Accession No. 77
NetworkMolecule = 9
Enzyme   = 4
Reaction  = 0
Molecule = 1
Enzyme   = 0
Reaction  = 0
Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80 ( Peer-reviewed publication )/
2006-12-12
   Related Pathway: 
62435566175139142182193211230317352366371377384390396402403409415421
432438444450456462468474480486492498504510516522528535541547553559565571
577583589595601607613619625631637643649655661667673679686692699704710716
722728734740746752758764770776782788794800806812818824830836842848854860
866872878884890896902908914921928934940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    This model is based on Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80. This is the feedforward model with MPK3 from figure 8a.
   
This pathway is part of accession 77 and is completely specified in the file acc77.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc77.g   
MATLAB format    acc77.m   
SBML format    acc77.xml   
15 MAPK
Pathway No. 352
 Ajay_Bhalla_
2004_Feedback_
Tuning

Accession No. 78
NetworkMolecule = 10
Enzyme   = 6
Reaction  = 0
Molecule = 1
Enzyme   = 0
Reaction  = 0
Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80. ( Peer-reviewed publication )/
2006-12-12
   Related Pathway: 
62435566175139142182193211230317335366371377384390396402403409415421
432438444450456462468474480486492498504510516522528535541547553559565571
577583589595601607613619625631637643649655661667673679686692699704710716
722728734740746752758764770776782788794800806812818824830836842848854860
866872878884890896902908914921928934940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    This model is taken from Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80. This is the feedback model from Figure 8a.
   
This pathway is part of accession 78 and is completely specified in the file acc78.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc78.g   
MATLAB format    acc78.m   
SBML format    acc78.xml   
16 MAPK
Pathway No. 366
 Ajay_Bhalla_
2007_Bistable

Accession No. 79
NetworkMolecule = 10
Enzyme   = 6
Reaction  = 0
Molecule = 1
Enzyme   = 0
Reaction  = 0
Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87/
2006-12-08
   Related Pathway: 
62435566175139142182193211230317335352371377384390396402403409415421
432438444450456462468474480486492498504510516522528535541547553559565571
577583589595601607613619625631637643649655661667673679686692699704710716
722728734740746752758764770776782788794800806812818824830836842848854860
866872878884890896902908914921928934940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    This is a model of ERKII signaling which is bistable due to feedback. The feedback occurs through ERKII phosphorylation of phospholipase A2 (PLA2), leading to increased production of arachidonic acid (AA), which activates protein kinase C (PKC) which activates c-Raf which is upstream of ERKII.
The model is a highly simplified variant of more detailed bistable models of MAPK signaling (Bhalla US, Iyengar R. Science. 1999 Jan 15;283(5400):381-7, Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80)
   
This pathway is part of accession 79 and is completely specified in the file acc79.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc79.g   
MATLAB format    acc79.m   
SBML format    acc79.xml   
17 MAPK
Pathway No. 371
 Ajay_Bhalla_
2007_PKM

Accession No. 80
NetworkMolecule = 10
Enzyme   = 6
Reaction  = 0
Molecule = 1
Enzyme   = 0
Reaction  = 0
Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87/
2006-12-08
   Related Pathway: 
62435566175139142182193211230317335352366377384390396402403409415421
432438444450456462468474480486492498504510516522528535541547553559565571
577583589595601607613619625631637643649655661667673679686692699704710716
722728734740746752758764770776782788794800806812818824830836842848854860
866872878884890896902908914921928934940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    This is a non-bistable model of ERKII signaling that also incorporates PKM synthesis triggered by Ca influx. It is a simplified variant of the model of Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80.
   
This pathway is part of accession 80 and is completely specified in the file acc80.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc80.g   
MATLAB format    acc80.m   
SBML format    acc80.xml   
18 MAPK
Pathway No. 377
 Ajay_bhalla_
2007_ReacDiff1_
1e-12

Accession No. 81
NetworkMolecule = 10
Enzyme   = 6
Reaction  = 0
Molecule = 1
Enzyme   = 0
Reaction  = 0
Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87/
2006-12-08
   Related Pathway: 
62435566175139142182193211230317335352366371384390396402403409415421
432438444450456462468474480486492498504510516522528535541547553559565571
577583589595601607613619625631637643649655661667673679686692699704710716
722728734740746752758764770776782788794800806812818824830836842848854860
866872878884890896902908914921928934940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    This is a 25-compartment reaction-diffusion version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 25 times. In addition, a subset (27 out of 42) molecules can diffuse between compartments. Diffusion is implemented as a reaction between corresponding molecules in neighboring compartments. For D = 1e-12 m^2/sec (i.e., 1 micron^2/sec ) the kf and kb of this reaction for these 10 micron compartments are both 0.01/sec. For D = 1e-13 m^2/sec (i.e., 0.1 micron^2/sec ) the kf and kb are 0.001/sec.
The stimulus file pkm_mapk22_diff_1e-12_Fig4A which was used for the model to replicate Figure 4A from the paper.
This stimulus file pkm_mapk22_diff_1e-12_Fig4G which was used for the model to replicate Figure 4G from the paper
   
This pathway is part of accession 81 and is completely specified in the file acc81.g.
There is no separate file for just this pathway.
FormatFile
Native Format (GENESIS format)    acc81.g   
19 MAPK
Pathway No. 384
 Ajay_bhalla_
2007_ReacDiff1_
1e-12

Accession No. 81
NetworkMolecule = 10
Enzyme   = 6
Reaction  = 0
Molecule = 1
Enzyme   = 0
Reaction  = 0
Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87/
2006-12-08
   Related Pathway: 
62435566175139142182193211230317335352366371377390396402403409415421
432438444450456462468474480486492498504510516522528535541547553559565571
577583589595601607613619625631637643649655661667673679686692699704710716
722728734740746752758764770776782788794800806812818824830836842848854860
866872878884890896902908914921928934940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    This is a 25-compartment reaction-diffusion version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 25 times. In addition, a subset (27 out of 42) molecules can diffuse between compartments. Diffusion is implemented as a reaction between corresponding molecules in neighboring compartments. For D = 1e-12 m^2/sec (i.e., 1 micron^2/sec ) the kf and kb of this reaction for these 10 micron compartments are both 0.01/sec. For D = 1e-13 m^2/sec (i.e., 0.1 micron^2/sec ) the kf and kb are 0.001/sec.
The stimulus file pkm_mapk22_diff_1e-12_Fig4A which was used for the model to replicate Figure 4A from the paper.
This stimulus file pkm_mapk22_diff_1e-12_Fig4G which was used for the model to replicate Figure 4G from the paper
   
This pathway is part of accession 81 and is completely specified in the file acc81.g.
There is no separate file for just this pathway.
FormatFile
Native Format (GENESIS format)    acc81.g   
20 MAPK
Pathway No. 390
 Ajay_bhalla_
2007_ReacDiff1_
1e-12

Accession No. 81
NetworkMolecule = 10
Enzyme   = 6
Reaction  = 0
Molecule = 1
Enzyme   = 0
Reaction  = 0
Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87/
2006-12-08
   Related Pathway: 
62435566175139142182193211230317335352366371377384396402403409415421
432438444450456462468474480486492498504510516522528535541547553559565571
577583589595601607613619625631637643649655661667673679686692699704710716
722728734740746752758764770776782788794800806812818824830836842848854860
866872878884890896902908914921928934940946952958960965971977983989995
100610121018102410301036104210481054106010661103
    This is a 25-compartment reaction-diffusion version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 25 times. In addition, a subset (27 out of 42) molecules can diffuse between compartments. Diffusion is implemented as a reaction between corresponding molecules in neighboring compartments. For D = 1e-12 m^2/sec (i.e., 1 micron^2/sec ) the kf and kb of this reaction for these 10 micron compartments are both 0.01/sec. For D = 1e-13 m^2/sec (i.e., 0.1 micron^2/sec ) the kf and kb are 0.001/sec.
The stimulus file pkm_mapk22_diff_1e-12_Fig4A which was used for the model to replicate Figure 4A from the paper.
This stimulus file pkm_mapk22_diff_1e-12_Fig4G which was used for the model to replicate Figure 4G from the paper
   
This pathway is part of accession 81 and is completely specified in the file acc81.g.
There is no separate file for just this pathway.
FormatFile
Native Format (GENESIS format)    acc81.g   

 
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Database compilation and code copyright (C) 2005, Upinder S. Bhalla and NCBS/TIFR
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