| |
Pathway Name
Pathway No. | Accession Name
Accession No. | Accession
Type | Pathway statistics | CamKII statistics | Source
Entry Date |
| 1 | Shared_Object_
fig3_CaMKII
Pathway No. 12 | fig3_CaMKII
Accession No. 2 | Network | Molecule = 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 |
| | #1Related 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. |
| Format | File | | Native Format (GENESIS format) | acc2.g | | GENESIS Format (Annotated version) | Anno_acc2.g |
|
| 2 | Shared_Object_
CaMKII_noPKA_
model3
Pathway No. 257 | CaMKII_noPKA_
model3
Accession No. 62 | Network | Molecule = 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 |
| | #1Related 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. |
|
| 3 | Shared_Object_
CaMKII_model3
Pathway No. 263 | CaMKII_model3
Accession No. 63 | Network | Molecule = 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 |
| | #1Related 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. |
|
| 4 | Shared_Object_
CaMKII_2003
Pathway No. 201 | CaMKII_2003
Accession No. 49 | Network | Molecule = 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 |
| | #1Related 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. |
|
| 5 | Shared_Object_
CaMKIII
Pathway No. 1093 | CaMKIII
Accession No. 90 | Network | Molecule = 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 |
| | #1Related 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. |
| Format | File | | Native Format (GENESIS format) | acc90.g |
|
| 6 | Shared_Object_
CaMKII
Pathway No. 172 | CaMKII
Accession No. 33 | Network | Molecule = 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 |
| | #1Related 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. |
| Format | File | | Native Format (GENESIS format) | acc33.g | | GENESIS Format (Annotated version) | Anno_acc33.g |
|
| 7 | Shared_Object_
AMPAR_CaMKII_
weak_coupling
Pathway No. 281 | AMPAR_CaMKII_
weak_coupling
Accession No. 65 | Network | Molecule = 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 |
| | #1Related 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. |
|
| 8 | Shared_Object_
AMPAR_CaMKII_
strong_coupling
Pathway No. 271 | AMPAR_CaMKII_
strong_coupling
Accession No. 64 | Network | Molecule = 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 |
| | #1Related 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. |
|
| 9 | PP1_CaMKII_PSD
Pathway No. 291 | AMPAR_CaMKII_
weak_coupling
Accession No. 65 | Network | Molecule = 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 |
| | #1Related 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. |
|
| 10 | CaMKII_PSD
Pathway No. 292 | AMPAR_CaMKII_
weak_coupling
Accession No. 65 | Network | Molecule = 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 |
| | #1Related 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. |
|
| 11 | CaMKII_g
Pathway No. 1138 | bcm
Accession No. 107 | Pathway | Molecule = 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 |
| | #2Related 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. |
|
| 12 | CaMKII_g
Pathway No. 1142 | bcm_bistable
Accession No. 108 | Pathway | Molecule = 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 |
| | #2Related 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. |
|
| 13 | CaMKIII_g
Pathway No. 1145 | syn_prot_
composite
Accession No. 109 | Pathway | Molecule = 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 23:58:38 |
| | #3Related Pathway:
1151, 1159 |
| | This model was used to generate fig 5 D to k, 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 109 and is completely specified in the file acc109.g.
There is no separate file for just this pathway. |
|
| 14 | CaMKIII_g
Pathway No. 1151 | aut6
Accession No. 110 | Pathway | Molecule = 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 |
| | #3Related 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. |
|
| 15 | CaMKIII_g
Pathway No. 1159 | syn_CaMKIII
Accession No. 114 | Pathway | Molecule = 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 |
| | #3Related 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. |
|
| 16 | CaMKII
Pathway No. 13 | fig3_CaMKII
Accession No. 2 | Network | Molecule = 9
Enzyme = 4
Reaction = 3
| Molecule = 8
Enzyme = 4
Reaction = 1
| Bhalla US and Iyengar R. Science (1999) 283(5400):381-7. ( peer-reviewed publication )/
2001-11-07 00:00:00 |
| | #19Related Pathway:
26, 80, 106, 121, 145, 159, 174, 202, 216, 235, 245, 258, 264, 272, 282, 322, 339, 357 |
| | 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. |
| Format | File | | Native Format (GENESIS format) | acc2.g | | GENESIS Format (Annotated version) | Anno_acc2.g |
|
| 17 | CaMKII
Pathway No. 26 | fig4_synapse
Accession No. 3 | Network | Molecule = 9
Enzyme = 4
Reaction = 3
| Molecule = 8
Enzyme = 4
Reaction = 1
| Bhalla US and Iyengar R. Science (1999) 283(5400):381-7. ( peer-reviewed publication )/
2001-11-07 00:00:00 |
| | #19Related Pathway:
13, 80, 106, 121, 145, 159, 174, 202, 216, 235, 245, 258, 264, 272, 282, 322, 339, 357 |
| | 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. |
| Format | File | | Native Format (GENESIS format) | acc3.g | | GENESIS Format (Annotated version) | Anno_acc3.g |
|
| 18 | CaMKII
Pathway No. 80 | Synaptic_
Network
Accession No. 16 | Network | Molecule = 9
Enzyme = 4
Reaction = 3
| Molecule = 8
Enzyme = 4
Reaction = 1
| Bhalla US and Iyengar R. Science (1999) 283(5400):381-7. ( peer-reviewed publication )/
2001-12-12 00:00:00 |
| | #19Related Pathway:
13, 26, 106, 121, 145, 159, 174, 202, 216, 235, 245, 258, 264, 272, 282, 322, 339, 357 |
| | Main reference here is the review by Hanson and Schulman, Ann Rev Biochem 1992 vol 61 pp 559-601. Most of the mechanistic details and a few constants are derived from there. Many kinetics are from Hanson and Schulman JBC 267:24 17216-17224 1992. The enzymes look a bit complicated. Actually it is just 3 reactions for different sites, by 4 states of CaMKII, defined by the phosphorylation state. This model approximates the fact that the enzyme is actually present as a decamer/dodecamer. It does so by treating the autophosphorylation reactions as being independent of the concentration of CaMKII. Also the rates for the autophosphorylation steps have been scaled to fit this approximation. |
| | 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. |
| Format | File | | Native Format (GENESIS format) | acc16.g | | GENESIS Format (Annotated version) | Anno_acc16.g |
|
| 19 | CaMKII
Pathway No. 106 | NonOsc_Ca_
IP3metabolism
Accession No. 23 | Network | Molecule = 10
Enzyme = 13
Reaction = 3
| Molecule = 8
Enzyme = 8
Reaction = 1
| Mishra J, Bhalla US. Biophys J. 2002 Sep;83(3):1298-316. ( peer-reviewed publication )/
2002-01-07 00:00:00 |
| | #19Related Pathway:
13, 26, 80, 121, 145, 159, 174, 202, 216, 235, 245, 258, 264, 272, 282, 322, 339, 357 |
| | Main reference here is the review by Hanson PI, Schulman H. Annu Rev Biochem. 1992;61:559-601. Most of the mechanistic details and a few constants are derived from there. Many kinetics are from Hanson PI, Schulman H. J Biol Chem. 1992 Aug 25;267(24):17216-24. The enzymes look a bit complicated. Actually it is just 3 reactions for different sites, by 4 states of CaMKII, defined by the phosphorylation state. This model approximates the fact that the enzyme is actually present as a decamer/dodecamer. It does so by treating the autophosphorylation reactions as being independent of the concentration of CaMKII. Also the rates for the autophosphorylation steps have been scaled to fit this approximation. |
| | This pathway is part of accession 23 and is completely specified in the file acc23.g.
There is no separate files for just this pathway. |
| Format | File | | Native Format (GENESIS format) | acc23.g | | GENESIS Format (Annotated version) | Anno_acc23.g |
|
| 20 | CaMKII
Pathway No. 121 | Osc_Ca_
IP3metabolism
Accession No. 24 | Network | Molecule = 10
Enzyme = 13
Reaction = 3
| Molecule = 8
Enzyme = 8
Reaction = 1
| Mishra J, Bhalla US. Biophys J. 2002 Sep;83(3):1298-316. ( peer-reviewed publication )/
2002-01-08 00:00:00 |
| | #19Related Pathway:
13, 26, 80, 106, 145, 159, 174, 202, 216, 235, 245, 258, 264, 272, 282, 322, 339, 357 |
| | Main reference here is the review by Hanson and Schulman, Ann Rev Biochem 1992 vol 61 pp 559-601. Most of the mechanistic details and a few constants are derived from there. Many kinetics are from Hanson and Schulman JBC 267:24 17216-17224 1992. The enzymes look a bit complicated. Actually it is just 3 reactions for different sites, by 4 states of CaMKII, defined by the phosphorylation state. This model approximates the fact that the enzyme is actually present as a decamer/dodecamer. It does so by treating the autophosphorylation reactions as being independent of the concentration of CaMKII. Also the rates for the autophosphorylation steps have been scaled to fit this approximation. |
| | This pathway is part of accession 24 and is completely specified in the file acc24.g.
There is no separate files for just this pathway. |
| Format | File | | Native Format (GENESIS format) | acc24.g | | GENESIS Format (Annotated version) | Anno_acc24.g |
|
or Pathway 