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Result: 1 - 14 of 14 rows are displayed

Pathway List for pp1

Default ordering is done according to Pathway Name.Table header can be used for changing the default ordering.
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Entries are color tagged depending on Network  or Pathway 
  Pathway Name
Pathway No.
Accession Name
Accession No.
Accession
Type
Pathway statisticspp1 statisticsSource
Entry Date
1 PP1
Pathway No. 15
 fig3_CaMKII

Accession No. 2
NetworkMolecule = 4
Enzyme   = 0
Reaction  = 2
Molecule = 0
Enzyme   = 0
Reaction  = 0
Bhalla US and Iyengar R. Science (1999) 283(5400):381-7. ( peer-reviewed publication )/
2001-11-07
   Related Pathway: 
2882204218237247260266274284324341359
    This is the model file for figure 3 from Bhalla US and Iyengar R. Science (1999) 283(5400):381-7. It is a model of the Ca activation of CaMKII and other CaM-activated enzymes. It includes the regulatory phosphatases PP1 and PP2B (Calcineurin) acting on CaMKII and also includes CaM-activated adenylyl cyclase and PKA in the synapse.
Demonstration script files for generating the figures in the paper, including figure 3, are available here.
   
This pathway is part of accession 2 and is completely specified in the file acc2.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc2.g   
GENESIS Format (Annotated version)    Anno_acc2.g   
2 PP1
Pathway No. 28
 fig4_synapse

Accession No. 3
NetworkMolecule = 4
Enzyme   = 0
Reaction  = 2
Molecule = 0
Enzyme   = 0
Reaction  = 0
Bhalla US and Iyengar R. Science (1999) 283(5400):381-7. ( peer-reviewed publication )/
2001-11-07
   Related Pathway: 
1582204218237247260266274284324341359
    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 PP1
Pathway No. 82
 Synaptic_
Network

Accession No. 16
NetworkMolecule = 4
Enzyme   = 0
Reaction  = 2
Molecule = 0
Enzyme   = 0
Reaction  = 0
Bhalla US and Iyengar R. Science (1999) 283(5400):381-7. ( peer-reviewed publication )/
2001-12-12
   Related Pathway: 
1528204218237247260266274284324341359
    Protein phosphatase 1. This is the primary dephosphorylating enzyme for CaMKII in this model. See Cohen and Cohen JBC 265(36):21435-21438 Cohen 1989 Ann Rev Biochem 58:453-508
   
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   
4 PP1
Pathway No. 204
 CaMKII_2003

Accession No. 49
NetworkMolecule = 4
Enzyme   = 0
Reaction  = 2
Molecule = 0
Enzyme   = 0
Reaction  = 0
Bhalla US. Biophys J. 2004 Aug;87(2):733-44. ( peer-reviewed publication )./
2003-04-28
   Related Pathway: 
152882218237247260266274284324341359
    Model of regulation of CaMKII by Calcium, including parallel excitatory input from CaM and inhibitory input from PP1 as regulated by Calcineurin and PKA. Cell type: neuronal.
Bhalla US. Biophys J. 2004 Aug;87(2):733-44.
   
This pathway is part of accession 49 and is completely specified in the file acc49.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc49.g   
GENESIS Format (Annotated version)    Anno_acc49.g   
MATLAB format    acc49.m   
SBML format    acc49.xml   
5 PP1
Pathway No. 218
 MAPK_network_
2003

Accession No. 50
NetworkMolecule = 4
Enzyme   = 0
Reaction  = 2
Molecule = 0
Enzyme   = 0
Reaction  = 0
Bhalla US Biophys J. 2004 Aug;87(2):745-53. ( peer-reviewed publication )/
2003-04-28
   Related Pathway: 
152882204237247260266274284324341359
    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
   
FormatFile
Native Format (GENESIS format)    path218.g   
GENESIS Format (Annotated version)    Anno_path218.g   
MATLAB format    path218.m   
6 PP1
Pathway No. 237
 AMPAR_traff_
model0

Accession No. 59
NetworkMolecule = 6
Enzyme   = 9
Reaction  = 2
Molecule = 0
Enzyme   = 0
Reaction  = 0
Hayer A, Bhalla US PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication )/
2005-07-19
   Related Pathway: 
152882204218247260266274284324341359
    This is model 0 from Hayer and Bhalla, PLoS Comput Biol 2005. It has a bistable model of AMPAR traffick, plus a non-bistable model of CaMKII. This differs from the reference model (model 1) in that model0 lacks degradation and turno ver reactions for AMPAR.
   
This pathway is part of accession 59 and is completely specified in the file acc59.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc59.g   
MATLAB format    acc59.m   
SBML format    acc59.xml   
7 PP1
Pathway No. 247
 AMPAR_traff_
model1

Accession No. 60
NetworkMolecule = 6
Enzyme   = 9
Reaction  = 2
Molecule = 0
Enzyme   = 0
Reaction  = 0
Hayer A, Bhalla US PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication )/
2005-07-19
   Related Pathway: 
152882204218237260266274284324341359
    This is the basic model of AMPAR trafficking bistability. It is based on Hayer and Bhalla, PLoS Comput. Biol. 2005. It includes the degradation and turnover of AMPARs. The CaMKII portion of the model is not bistable.
   
This pathway is part of accession 60 and is completely specified in the file acc60.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc60.g   
MATLAB format    acc60.m   
SBML format    acc60.xml   
8 PP1
Pathway No. 260
 CaMKII_noPKA_
model3

Accession No. 62
NetworkMolecule = 4
Enzyme   = 0
Reaction  = 2
Molecule = 0
Enzyme   = 0
Reaction  = 0
Hayer A, Bhalla US PLoS PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication )/
2005-07-19
   Related Pathway: 
152882204218237247266274284324341359
    This is the model of CaMKII bistability, model 3. It exhibits bistability in CaMKII activation due to autophosphorylation at the PSD and local saturation of PP1. This version of model 3 does not include the full PKA regulatory pathway, and instead has a predefined initial amount of active PKA.
   
This pathway is part of accession 62 and is completely specified in the file acc62.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc62.g   
MATLAB format    acc62.m   
SBML format    acc62.xml   
9 PP1
Pathway No. 266
 CaMKII_model3

Accession No. 63
NetworkMolecule = 4
Enzyme   = 0
Reaction  = 2
Molecule = 0
Enzyme   = 0
Reaction  = 0
Hayer A, Bhalla US PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication )/
2005-07-19
   Related Pathway: 
152882204218237247260274284324341359
    This is the complete model of CaMKII bistability, model 3. It exhibits bistability in CaMKII activation due to autophosphorylation at the PSD and local saturation of PP1. This version of model 3 includes PKA regulatory input. This has little effect on the deterministic calculations, but the PKA pathway introduces a lot of noise which causes a difference in stochastic runs.
   
This pathway is part of accession 63 and is completely specified in the file acc63.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc63.g   
MATLAB format    acc63.m   
SBML format    acc63.xml   
10 PP1
Pathway No. 274
 AMPAR_CaMKII_
strong_coupling

Accession No. 64
NetworkMolecule = 4
Enzyme   = 0
Reaction  = 2
Molecule = 0
Enzyme   = 0
Reaction  = 0
Hayer A, Bhalla US PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication )/
2005-07-19
   Related Pathway: 
152882204218237247260266284324341359
    This is a model of tight coupling between the AMPAR trafficking bistability, and the CaMKII autophosphorylation bistability. In this model, the CaMKII activity is self sustaining only when AMPAR is turned on. Further, CaMKII turns on when AMPAR is turned on.
   
This pathway is part of accession 64 and is completely specified in the file acc64.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc64.g   
MATLAB format    acc64.m   
SBML format    acc64.xml   
11 PP1
Pathway No. 284
 AMPAR_CaMKII_
weak_coupling

Accession No. 65
NetworkMolecule = 4
Enzyme   = 0
Reaction  = 2
Molecule = 0
Enzyme   = 0
Reaction  = 0
Hayer A, Bhalla US PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication )/
2005-07-21
   Related Pathway: 
152882204218237247260266274324341359
    This is a model of weak coupling between the AMPAR traffikcing bistability, and the CaMKII autophosphorylation bistability. In this model, there are three stable states: Both off, AMPAR on, or both on. The fourth possible state: CaMKII on but AMPAR off, is not truly stable, since over the course of hours the AMPAR also turns on.
   
This pathway is part of accession 65 and is completely specified in the file acc65.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc65.g   
MATLAB format    acc65.m   
SBML format    acc65.xml   
12 PP1
Pathway No. 324
 Ajay_Bhalla_
2004_PKM_Tuning

Accession No. 76
NetworkMolecule = 4
Enzyme   = 0
Reaction  = 2
Molecule = 0
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: 
152882204218237247260266274284341359
    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   
13 PP1
Pathway No. 341
 Ajay_Bhalla_
2004_PKM_MKP3_
Tuning

Accession No. 77
NetworkMolecule = 4
Enzyme   = 0
Reaction  = 2
Molecule = 0
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: 
152882204218237247260266274284324359
    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   
14 PP1
Pathway No. 359
 Ajay_Bhalla_
2004_Feedback_
Tuning

Accession No. 78
NetworkMolecule = 4
Enzyme   = 0
Reaction  = 2
Molecule = 0
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: 
152882204218237247260266274284324341
    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   

 
Result: 1 - 14 of 14 rows are displayed



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