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Pathway List for CamKII

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 
#3#3#2#2#1#1#1#1#1#1#1#1#1#1
  Pathway Name
Pathway No.		Accession Name
Accession No.		Accession
Type		Pathway statisticsCamKII statisticsSource
Entry Date
21 CaMKIII_g
Pathway No. 1151		 aut6

Accession No. 110		PathwayMolecule = 3
Enzyme   = 0
Reaction  = 0
Molecule = 3
Enzyme   = 0
Reaction  = 0
Bhalla US. PLoS Comput Biol 2021 Nov 29;17(11):e1009621. /
2022-10-01 00:02:13
   Related Pathway: 
1145, 1159
    This model was used to generate Fig 6 in Bhalla US. HillTau: A fast, compact abstraction for model reduction in biochemical signaling networks. PLoS Comput Biol 2021 Nov 29;17(11):e1009621.
   
This pathway is part of accession 110 and is completely specified in the file acc110.g.
There is no separate file for just this pathway.
FormatFile
HillTau format    acc110.json   
22 CaMKIII_g
Pathway No. 1159		 syn_CaMKIII

Accession No. 114		PathwayMolecule = 2
Enzyme   = 0
Reaction  = 0
Molecule = 2
Enzyme   = 0
Reaction  = 0
Bhalla US. PLoS Comput Biol 2021 Nov 29;17(11):e1009621. /
2022-10-01 00:12:23
   Related Pathway: 
1145, 1151
    This model was used to generate Fig 3 supp A to F in Bhalla US. HillTau: A fast, compact abstraction for model reduction in biochemical signaling networks. PLoS Comput Biol 2021 Nov 29;17(11):e1009621.
   
This pathway is part of accession 114 and is completely specified in the file acc114.g.
There is no separate file for just this pathway.
FormatFile
HillTau format    acc114.json   
23 CaMKII_g
Pathway No. 1138		 bcm

Accession No. 107		PathwayMolecule = 2
Enzyme   = 0
Reaction  = 0
Molecule = 2
Enzyme   = 0
Reaction  = 0
Bhalla US.PLoS Comput Biol 2021 Nov 29;17(11):e1009621./
2022-09-30 23:36:25
   Related Pathway: 
1142
    This model was used to generate Fig 3 C, D ,E, Fig 6,Fig7 supp C in Bhalla US. HillTau: A fast, compact abstraction for model reduction in biochemical signaling networks. PLoS Comput Biol 2021 Nov 29;17(11):e1009621.
   
This pathway is part of accession 107 and is completely specified in the file acc107.g.
There is no separate file for just this pathway.
FormatFile
HillTau format    acc107.json   
24 CaMKII_g
Pathway No. 1142		 bcm_bistable

Accession No. 108		PathwayMolecule = 4
Enzyme   = 0
Reaction  = 0
Molecule = 3
Enzyme   = 0
Reaction  = 0
Bhalla US. PLoS Comput Biol 2021 Nov 29;17(11):e1009621. /
2022-09-30 23:49:58
   Related Pathway: 
1138
    This model was used to generate Fig 3 G in Bhalla US. HillTau: A fast, compact abstraction for model reduction in biochemical signaling networks. PLoS Comput Biol 2021 Nov 29;17(11):e1009621.
   
This pathway is part of accession 108 and is completely specified in the file acc108.g.
There is no separate file for just this pathway.
FormatFile
HillTau format    acc108.json   
25 CaMKII_PSD
Pathway No. 292		 AMPAR_CaMKII_
weak_coupling
Accession No. 65		NetworkMolecule = 14
Enzyme   = 22
Reaction  = 8
Molecule = 11
Enzyme   = 19
Reaction  = 4
Hayer A, Bhalla US PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication )/
2005-07-21 00:00:00
   Related Pathway: ------
    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   
26 PP1_CaMKII_PSD
Pathway No. 291		 AMPAR_CaMKII_
weak_coupling
Accession No. 65		NetworkMolecule = 1
Enzyme   = 5
Reaction  = 0
Molecule = 1
Enzyme   = 5
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 00:00:00
   Related Pathway: ------
    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   
27 
  • Shared_Object_
    AMPAR_CaMKII_
    strong_coupling
    Pathway No. 271
    		•  AMPAR_CaMKII_
    strong_coupling
    Accession No. 64    		NetworkMolecule = 51
    Enzyme   = 148
    Reaction  = 16
    		Molecule = 14
    Enzyme   = 19
    Reaction  = 4
    		Hayer A, Bhalla US PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication )/
    2005-07-19 00:00:00
       Related Pathway: ------
        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   
    28 
  • Shared_Object_
    AMPAR_CaMKII_
    weak_coupling
    Pathway No. 281
    		•  AMPAR_CaMKII_
    weak_coupling
    Accession No. 65    		NetworkMolecule = 30
    Enzyme   = 14
    Reaction  = 8
    		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 00:00:00
       Related Pathway: ------
        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   
    29 
  • Shared_Object_
    CaMKII
    Pathway No. 172
    		•  CaMKII

    Accession No. 33    		NetworkMolecule = 1
    Enzyme   = 0
    Reaction  = 0
    		Molecule = 0
    Enzyme   = 0
    Reaction  = 0
    		William R. Holmes J Comput Neurosci. (2000) 8(1):65-85 ( peer-reviewed publication )/
    2002-08-21 00:00:00
       Related Pathway: ------
        This is a deterministic, point kinetics approximation to the dendritic spine CaMKII model described in William R. Holmes J Comput Neurosci. (2000) 8(1):65-85. Rates are the same but the responses differ somewhat because this model does not include the stochastic and diffusive calculations of the original.
       
    This pathway is part of accession 33 and is completely specified in the file acc33.g.
    There is no separate files for just this pathway.
    FormatFile
    Native Format (GENESIS format)    acc33.g   
    GENESIS Format (Annotated version)    Anno_acc33.g   
    30 
  • Shared_Object_
    CaMKIII
    Pathway No. 1093
    		•  CaMKIII

    Accession No. 90    		NetworkMolecule = 15
    Enzyme   = 5
    Reaction  = 3
    		Molecule = 4
    Enzyme   = 4
    Reaction  = 2
    		Jain P, and Bhalla, U.S. PLoS Comput Biol. 2009 Feb;5(2). ( Peer-reviewed publication )/
    2009-02-12 00:00:00
       Related Pathway: ------
        CaMKIII is activated by Ca2+ and inactivated by S6K. Since CaMKIII inhibits eEF2, the net effect of Ca2+ on elongation is inhibitory and of S6K is excitatory
       
    This pathway is part of accession 90 and is completely specified in the file acc90.g.
    There is no separate file for just this pathway.
    FormatFile
    Native Format (GENESIS format)    acc90.g   
    31 
  • Shared_Object_
    CaMKII_2003
    Pathway No. 201
    		•  CaMKII_2003

    Accession No. 49    		NetworkMolecule = 10
    Enzyme   = 14
    Reaction  = 0
    		Molecule = 0
    Enzyme   = 0
    Reaction  = 0
    		Bhalla US. Biophys J. 2004 Aug;87(2):733-44. ( peer-reviewed publication )./
    2003-04-28 00:00:00
       Related Pathway: ------
        Based on nonscaf_syn1.g. Stripped out everything except stuff which directly controls CaMKII. Designed to do doser of CaMKII vs Ca.
       
    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   
    32 
  • Shared_Object_
    CaMKII_model3
    Pathway No. 263
    		•  CaMKII_model3

    Accession No. 63    		NetworkMolecule = 36
    Enzyme   = 30
    Reaction  = 14
    		Molecule = 14
    Enzyme   = 3
    Reaction  = 4
    		Hayer A, Bhalla US PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication )/
    2005-07-19 00:00:00
       Related Pathway: ------
        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   
    33 
  • Shared_Object_
    CaMKII_noPKA_
    model3
    Pathway No. 257
    		•  CaMKII_noPKA_
    model3
    Accession No. 62    		NetworkMolecule = 33
    Enzyme   = 28
    Reaction  = 13
    		Molecule = 14
    Enzyme   = 3
    Reaction  = 4
    		Hayer A, Bhalla US PLoS PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication )/
    2005-07-19 00:00:00
       Related Pathway: ------
        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   
    34 
  • Shared_Object_
    fig3_CaMKII
    Pathway No. 12
    		•  fig3_CaMKII

    Accession No. 2    		NetworkMolecule = 15
    Enzyme   = 16
    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 00:00:00
       Related Pathway: ------
        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   
     
    Result: 21 - 34 of 34 rows are displayed Previous of 2  Next


    Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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