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Pathway Name Pathway No. | Accession Name Accession No. | Accession Type | Pathway statistics | CamKII statistics | Source Entry Date |
1 | 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. |
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2 | 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. |
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3 | 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. |
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4 | 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. |
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5 | 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. |
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6 | 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 |
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7 | 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 |
|
8 | 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 |
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9 | 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 |
|
10 | 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 |
|
11 | 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 |
|
12 | CaMKII Pathway No. 145 | NonOsc_Ca_ IP3metabolism Accession No. 31 | 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 )/ 2002-04-03 00:00:00 |
| #19Related Pathway: 13, 26, 80, 106, 121, 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 31 and is completely specified in the file acc31.g. There is no separate files for just this pathway. |
Format | File | Native Format (GENESIS format) | acc31.g | GENESIS Format (Annotated version) | Anno_acc31.g |
|
13 | CaMKII Pathway No. 159 | Osc_Ca_ IP3metabolism Accession No. 32 | 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 )/ 2002-04-03 00:00:00 |
| #19Related Pathway: 13, 26, 80, 106, 121, 145, 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 32 and is completely specified in the file acc32.g. There is no separate files for just this pathway. |
Format | File | Native Format (GENESIS format) | acc32.g | GENESIS Format (Annotated version) | Anno_acc32.g |
|
14 | 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 |
|
15 | CaMKII Pathway No. 174 | CaMKII
Accession No. 33 | Network | Molecule = 11 Enzyme = 2 Reaction = 14
| Molecule = 8 Enzyme = 2 Reaction = 9
| William R. Holmes J Comput Neurosci. (2000) 8(1):65-85 ( peer-reviewed publication )/ 2002-08-21 00:00:00 |
| #19Related Pathway: 13, 26, 80, 106, 121, 145, 159, 202, 216, 235, 245, 258, 264, 272, 282, 322, 339, 357 |
| 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. |
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16 | 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. |
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17 | CaMKII Pathway No. 202 | CaMKII_2003
Accession No. 49 | Network | Molecule = 8 Enzyme = 4 Reaction = 3
| Molecule = 7 Enzyme = 4 Reaction = 1
| Bhalla US. Biophys J. 2004 Aug;87(2):733-44. ( peer-reviewed publication )./ 2003-04-28 00:00:00 |
| #19Related Pathway: 13, 26, 80, 106, 121, 145, 159, 174, 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 enzs look a terrible mess. Actually it is just 3 reactions for diff sites, by 4 states of CaMKII, defined by the phosph state. |
| 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. |
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18 | CaMKII Pathway No. 216 | MAPK_network_ 2003 Accession No. 50 | Network | Molecule = 8 Enzyme = 4 Reaction = 3
| Molecule = 7 Enzyme = 4 Reaction = 1
| Bhalla US Biophys J. 2004 Aug;87(2):745-53. ( peer-reviewed publication )/ 2003-04-28 00:00:00 |
| #19Related Pathway: 13, 26, 80, 106, 121, 145, 159, 174, 202, 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 enzs look a terrible mess. Actually it is just 3 reactions for diff sites, by 4 states of CaMKII, defined by the phosph state. |
| |
19 | CaMKII Pathway No. 235 | AMPAR_traff_ model0 Accession No. 59 | Network | Molecule = 25 Enzyme = 24 Reaction = 10
| Molecule = 21 Enzyme = 22 Reaction = 5
| 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 |
| #19Related Pathway: 13, 26, 80, 106, 121, 145, 159, 174, 202, 216, 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 enzs look a terrible mess. Actually it is just 3 reactions for diff sites, by 4 states of CaMKII, defined by the phosph state. |
| 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. |
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20 | CaMKII Pathway No. 245 | AMPAR_traff_ model1 Accession No. 60 | Network | Molecule = 25 Enzyme = 24 Reaction = 10
| Molecule = 21 Enzyme = 22 Reaction = 5
| 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 |
| #19Related Pathway: 13, 26, 80, 106, 121, 145, 159, 174, 202, 216, 235, 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 enzs look a terrible mess. Actually it is just 3 reactions for diff sites, by 4 states of CaMKII, defined by the phosph state. |
| 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. |
|