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Result: 1 - 14 of 14 rows are displayed

Pathway List for ac

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 statisticsac statisticsSource
Entry Date
1 AC
Pathway No. 18
 fig3_CaMKII

Accession No. 2
NetworkMolecule = 13
Enzyme   = 9
Reaction  = 7
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: 
3185136197221241251269278289327344362
    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 AC
Pathway No. 31
 fig4_synapse

Accession No. 3
NetworkMolecule = 13
Enzyme   = 9
Reaction  = 7
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: 
1885136197221241251269278289327344362
    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 AC
Pathway No. 85
 Synaptic_
Network

Accession No. 16
NetworkMolecule = 13
Enzyme   = 9
Reaction  = 7
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: 
1831136197221241251269278289327344362
    The adenylyl cyclase module currently represents only two isoforms: AC1 and AC2. There are at least 8 forms of AC known: Pieroni et al 1993 Curr Op Neurobiol 3:345-351. AC1 is stimulated by CaM, and AC2 by phosphorylation by PKC, in addition to the usual Gs stimulation. A more recent thorough review is Defer et al 2000 Am J Physiol Renal Physiol 279:F400-F416 This model does not incorporate effects such as GAP activity of the cyclases.
   
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 AC
Pathway No. 136
 cAMP_pathway

Accession No. 25
NetworkMolecule = 6
Enzyme   = 3
Reaction  = 2
Molecule = 1
Enzyme   = 0
Reaction  = 0
Bhalla US Methods Enzymol. 2002;345:3-23). ( peer-reviewed publication )/
2002-01-12
   Related Pathway: 
183185197221241251269278289327344362
    Adenylyl cyclase, also known as adenylate cyclase. There are some ten isoforms, but here I represent only the canonical Gs-stimulated activity.
   
FormatFile
Native Format (GENESIS format)    path136.g   
GENESIS Format (Annotated version)    Anno_path136.g   
MATLAB format    path136.m   
5 AC
Pathway No. 197
 PKA_2003

Accession No. 47
NetworkMolecule = 6
Enzyme   = 3
Reaction  = 2
Molecule = 1
Enzyme   = 0
Reaction  = 0
Bhalla US. (2004) Biophys J. 87(2):733-44. ( peer-reviewed publication )/
2003-04-28
   Related Pathway: 
183185136221241251269278289327344362
    Adenylyl cyclase, also known as adenylate cyclase. There are some ten isoforms, but here I represent only the canonical Gs-stimulated activity.
   
FormatFile
Native Format (GENESIS format)    path197.g   
GENESIS Format (Annotated version)    Anno_path197.g   
MATLAB format    path197.m   
6 AC
Pathway No. 221
 MAPK_network_
2003

Accession No. 50
NetworkMolecule = 13
Enzyme   = 9
Reaction  = 7
Molecule = 0
Enzyme   = 0
Reaction  = 0
Bhalla US Biophys J. 2004 Aug;87(2):745-53. ( peer-reviewed publication )/
2003-04-28
   Related Pathway: 
183185136197241251269278289327344362
    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)    path221.g   
GENESIS Format (Annotated version)    Anno_path221.g   
MATLAB format    path221.m   
7 AC
Pathway No. 241
 AMPAR_traff_
model0

Accession No. 59
NetworkMolecule = 12
Enzyme   = 6
Reaction  = 5
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: 
183185136197221251269278289327344362
    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   
8 AC
Pathway No. 251
 AMPAR_traff_
model1

Accession No. 60
NetworkMolecule = 12
Enzyme   = 6
Reaction  = 5
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: 
183185136197221241269278289327344362
    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   
9 AC
Pathway No. 269
 CaMKII_model3

Accession No. 63
NetworkMolecule = 11
Enzyme   = 6
Reaction  = 5
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: 
183185136197221241251278289327344362
    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 AC
Pathway No. 278
 AMPAR_CaMKII_
strong_coupling

Accession No. 64
NetworkMolecule = 11
Enzyme   = 6
Reaction  = 5
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: 
183185136197221241251269289327344362
    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 AC
Pathway No. 289
 AMPAR_CaMKII_
weak_coupling

Accession No. 65
NetworkMolecule = 11
Enzyme   = 6
Reaction  = 5
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: 
183185136197221241251269278327344362
    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 AC
Pathway No. 327
 Ajay_Bhalla_
2004_PKM_Tuning

Accession No. 76
NetworkMolecule = 13
Enzyme   = 9
Reaction  = 7
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: 
183185136197221241251269278289344362
    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 AC
Pathway No. 344
 Ajay_Bhalla_
2004_PKM_MKP3_
Tuning

Accession No. 77
NetworkMolecule = 13
Enzyme   = 9
Reaction  = 7
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: 
183185136197221241251269278289327362
    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 AC
Pathway No. 362
 Ajay_Bhalla_
2004_Feedback_
Tuning

Accession No. 78
NetworkMolecule = 13
Enzyme   = 9
Reaction  = 7
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: 
183185136197221241251269278289327344
    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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