| |
Name /
Accession
No. | Accession Type /
Entry Date | Accession statistics | CamKII statistics | Species /
Tissue | Cell Compartment /
Source | Methodology /
Model_
Implementation |
| 11 | MAPK_network_
2003
Accession No. : 50 | Network /
2003-04-28 00:00:00 | Molecule = 133
Enzyme = 62
Reaction = 79
| Molecule = 7
Enzyme = 4
Reaction = 1
| Generic mammalian /
Brain - Neuronal | Synapse /
Bhalla US Biophys J. 2004 Aug;87(2):745-53. ( peer-reviewed publication ) | Qualitative /
Exact GENESIS implementation |
| | 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 |
| | |
| 12 | AMPAR_traff_
model0
Accession No. : 59 | Network /
2005-07-19 00:00:00 | Molecule = 130
Enzyme = 156
Reaction = 52
| Molecule = 21
Enzyme = 22
Reaction = 5
| General Mammalian /
Neuronal | Synaptic Spine, Postsynaptic Density /
Hayer A, Bhalla US PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication ) | Quantitative match to experiments /
Exact GENESIS implementation |
| | 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. |
| | |
| 13 | AMPAR_traff_
model1
Accession No. : 60 | Network /
2005-07-19 00:00:00 | Molecule = 132
Enzyme = 156
Reaction = 57
| Molecule = 21
Enzyme = 22
Reaction = 5
| General Mammalian /
Neuronal | Synaptic Spine, Postsynaptic Density /
Hayer A, Bhalla US PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication ) | Quantitative match to experiments /
Exact GENESIS implementation |
| | 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. |
| | |
| 14 | CaMKII_noPKA_
model3
Accession No. : 62 | Network /
2005-07-19 00:00:00 | Molecule = 53
Enzyme = 32
Reaction = 26
| Molecule = 21
Enzyme = 7
Reaction = 5
| General Mammalian /
Neuronal | Synaptic Spine, Postsynaptic Density /
Hayer A, Bhalla US PLoS PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication ) | Quantitative match to experiments, Qualitative /
Exact GENESIS implementation |
| | 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. |
| | |
| 15 | CaMKII_model3
Accession No. : 63 | Network /
2005-07-19 00:00:00 | Molecule = 76
Enzyme = 40
Reaction = 39
| Molecule = 21
Enzyme = 7
Reaction = 5
| General Mammalian /
Neuronal | Synaptic Spine, Postsynaptic Density /
Hayer A, Bhalla US PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication ) | Quantitative match to experiments, Qualitative /
Exact GENESIS implementation |
| | 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. |
| | |
| 16 | AMPAR_CaMKII_
strong_coupling
Accession No. : 64 | Network /
2005-07-19 00:00:00 | Molecule = 133
Enzyme = 158
Reaction = 57
| Molecule = 21
Enzyme = 23
Reaction = 5
| General Mammalian /
Neuronal | Synaptic Spine, Postsynaptic Density /
Hayer A, Bhalla US PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication ) | Quantitative match to experiments, Qualitative /
Exact GENESIS implementation |
| | 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. |
| | |
| 17 | AMPAR_CaMKII_
weak_coupling
Accession No. : 65 | Network /
2005-07-21 00:00:00 | Molecule = 134
Enzyme = 158
Reaction = 57
| Molecule = 22
Enzyme = 28
Reaction = 5
| General Mammalian /
Neuronal | Synaptic Spine, Postsynaptic Density /
Hayer A, Bhalla US PLoS Comput Biol. 2005 Jul;1(2):137-54. Epub 2005 Jul 29. ( Peer-reviewed publication ) | Quantitative match to experiments, Qualitative /
Exact GENESIS implementation |
| | 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. |
| | |
| 18 | Ajay_Bhalla_
2004_PKM_Tuning
Accession No. : 76 | Network /
2006-12-12 00:00:00 | Molecule = 137
Enzyme = 66
Reaction = 79
| Molecule = 7
Enzyme = 4
Reaction = 1
| Rat /
Hippocampal CA1 | Dendrite /
Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80. ( Peer-reviewed publication ) | Semi -Quantitative match to experiments /
Exact GENESIS implementation |
| | 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. |
| | |
| 19 | Ajay_Bhalla_
2004_PKM_MKP3_
Tuning
Accession No. : 77 | Network /
2006-12-12 00:00:00 | Molecule = 141
Enzyme = 66
Reaction = 81
| Molecule = 7
Enzyme = 4
Reaction = 1
| Rat /
Hippocampal CA1 | Dendrite /
Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80 ( Peer-reviewed publication ) | Semi-Quantitative match to experiments /
Exact GENESIS implementation |
| | 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. |
| | |
| 20 | Ajay_Bhalla_
2004_Feedback_
Tuning
Accession No. : 78 | Network /
2006-12-12 00:00:00 | Molecule = 135
Enzyme = 64
Reaction = 81
| Molecule = 7
Enzyme = 4
Reaction = 1
| Rat /
Hippocampal CA1 | Dendrites /
Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80. ( Peer-reviewed publication ) | Semi-Quantitative match to experiments /
Exact GENESIS implementation |
| | 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. |
| | |
indicates that ordering is done according to ascending or descending order.
or Pathway 