| |
Pathway Name
Pathway No. | Accession Name
Accession No. | Accession
Type | Pathway statistics | pp1 statistics | Source
Entry Date |
| 1 | PP1
Pathway No. 359 | Ajay_Bhalla_
2004_Feedback_
Tuning
Accession No. 78 | Network | Molecule = 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 00:00:00 |
| | #14Related Pathway:
15, 28, 82, 204, 218, 237, 247, 260, 266, 274, 284, 324, 341 |
| | 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. |
|
| 2 | PP1
Pathway No. 341 | Ajay_Bhalla_
2004_PKM_MKP3_
Tuning
Accession No. 77 | Network | Molecule = 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 00:00:00 |
| | #14Related Pathway:
15, 28, 82, 204, 218, 237, 247, 260, 266, 274, 284, 324, 359 |
| | 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. |
|
| 3 | PP1
Pathway No. 324 | Ajay_Bhalla_
2004_PKM_Tuning
Accession No. 76 | Network | Molecule = 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 00:00:00 |
| | #14Related Pathway:
15, 28, 82, 204, 218, 237, 247, 260, 266, 274, 284, 341, 359 |
| | 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. |
|
| 4 | PP1
Pathway No. 284 | AMPAR_CaMKII_
weak_coupling
Accession No. 65 | Network | Molecule = 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 00:00:00 |
| | #14Related Pathway:
15, 28, 82, 204, 218, 237, 247, 260, 266, 274, 324, 341, 359 |
| | 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. |
|
| 5 | PP1
Pathway No. 274 | AMPAR_CaMKII_
strong_coupling
Accession No. 64 | Network | Molecule = 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 00:00:00 |
| | #14Related Pathway:
15, 28, 82, 204, 218, 237, 247, 260, 266, 284, 324, 341, 359 |
| | 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. |
|
| 6 | PP1
Pathway No. 266 | CaMKII_model3
Accession No. 63 | Network | Molecule = 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 00:00:00 |
| | #14Related Pathway:
15, 28, 82, 204, 218, 237, 247, 260, 274, 284, 324, 341, 359 |
| | 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. |
|
| 7 | PP1
Pathway No. 260 | CaMKII_noPKA_
model3
Accession No. 62 | Network | Molecule = 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 00:00:00 |
| | #14Related Pathway:
15, 28, 82, 204, 218, 237, 247, 266, 274, 284, 324, 341, 359 |
| | 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. |
|
| 8 | PP1
Pathway No. 247 | AMPAR_traff_
model1
Accession No. 60 | Network | Molecule = 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 00:00:00 |
| | #14Related Pathway:
15, 28, 82, 204, 218, 237, 260, 266, 274, 284, 324, 341, 359 |
| | 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. |
|
| 9 | PP1
Pathway No. 237 | AMPAR_traff_
model0
Accession No. 59 | Network | Molecule = 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 00:00:00 |
| | #14Related Pathway:
15, 28, 82, 204, 218, 247, 260, 266, 274, 284, 324, 341, 359 |
| | 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. |
|
| 10 | PP1
Pathway No. 218 | MAPK_network_
2003
Accession No. 50 | Network | Molecule = 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 00:00:00 |
| | #14Related Pathway:
15, 28, 82, 204, 237, 247, 260, 266, 274, 284, 324, 341, 359 |
| | 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 |
| | |
| 11 | PP1
Pathway No. 204 | CaMKII_2003
Accession No. 49 | Network | Molecule = 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 00:00:00 |
| | #14Related Pathway:
15, 28, 82, 218, 237, 247, 260, 266, 274, 284, 324, 341, 359 |
| | 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. |
|
| 12 | PP1
Pathway No. 82 | Synaptic_
Network
Accession No. 16 | Network | Molecule = 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 00:00:00 |
| | #14Related Pathway:
15, 28, 204, 218, 237, 247, 260, 266, 274, 284, 324, 341, 359 |
| | 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. |
| Format | File | | Native Format (GENESIS format) | acc16.g | | GENESIS Format (Annotated version) | Anno_acc16.g |
|
| 13 | PP1
Pathway No. 28 | fig4_synapse
Accession No. 3 | Network | Molecule = 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 00:00:00 |
| | #14Related Pathway:
15, 82, 204, 218, 237, 247, 260, 266, 274, 284, 324, 341, 359 |
| | 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 |
|
| 14 | PP1
Pathway No. 15 | fig3_CaMKII
Accession No. 2 | Network | Molecule = 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 00:00:00 |
| | #14Related Pathway:
28, 82, 204, 218, 237, 247, 260, 266, 274, 284, 324, 341, 359 |
| | 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 |
|
or Pathway 