| |
Pathway Name
Pathway No. | Accession Name
Accession No. | Accession
Type | Pathway statistics | pka statistics | Source
Entry Date |
| 1 | PKA
Pathway No. 17 | fig3_CaMKII
Accession No. 2 | Network | Molecule = 9
Enzyme = 0
Reaction = 7
| 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:
30, 84, 135, 196, 220, 240, 250, 270, 277, 288, 326, 343, 361 |
| | 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 | PKA
Pathway No. 30 | fig4_synapse
Accession No. 3 | Network | Molecule = 9
Enzyme = 0
Reaction = 7
| 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:
17, 84, 135, 196, 220, 240, 250, 270, 277, 288, 326, 343, 361 |
| | 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 |
|
| 3 | PKA
Pathway No. 326 | Ajay_Bhalla_
2004_PKM_Tuning
Accession No. 76 | Network | Molecule = 9
Enzyme = 0
Reaction = 7
| 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:
17, 30, 84, 135, 196, 220, 240, 250, 270, 277, 288, 343, 361 |
| | General ref: Taylor et al Ann Rev Biochem 1990 59:971-1005 |
| | 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 | PKA
Pathway No. 361 | Ajay_Bhalla_
2004_Feedback_
Tuning
Accession No. 78 | Network | Molecule = 9
Enzyme = 0
Reaction = 7
| 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:
17, 30, 84, 135, 196, 220, 240, 250, 270, 277, 288, 326, 343 |
| | General ref: Taylor et al Ann Rev Biochem 1990 59:971-1005 |
| | 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. |
|
| 5 | PKA
Pathway No. 343 | Ajay_Bhalla_
2004_PKM_MKP3_
Tuning
Accession No. 77 | Network | Molecule = 9
Enzyme = 0
Reaction = 7
| 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:
17, 30, 84, 135, 196, 220, 240, 250, 270, 277, 288, 326, 361 |
| | General ref: Taylor et al Ann Rev Biochem 1990 59:971-1005 |
| | 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. |
|
| 6 | PKA
Pathway No. 84 | Synaptic_
Network
Accession No. 16 | Network | Molecule = 9
Enzyme = 0
Reaction = 7
| 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:
17, 30, 135, 196, 220, 240, 250, 270, 277, 288, 326, 343, 361 |
| | Protein kinase A. It has two regulatory and two catalytic subunits, represented here as R2C2. Each regulatory subunit binds two cAMPs. I also model an inhibitor of PKA which binds stoichiometrically and thus sharpens the response curve for PKA against cAMP. General reference: Taylor et al Ann Rev Biochem 1990 59:971-1005 Other references Ogreid and Doskeland 1983 Biochem 22:1686-1696 is a great, detailed paper. Also: Ogreid and Doskeland 1982 FEBS Lett 150(1):161-166 Ogreid et al 1983 JBC 258(2):1041-1049 Robinson-Steiner and Corbin 1983 JBC 258(2):1032-1040 Hasler et al 1992 FASEB J 6:2735-2741 |
| | 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 |
|
| 7 | PKA
Pathway No. 220 | MAPK_network_
2003
Accession No. 50 | Network | Molecule = 9
Enzyme = 0
Reaction = 7
| 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:
17, 30, 84, 135, 196, 240, 250, 270, 277, 288, 326, 343, 361 |
| | General ref: Taylor et al Ann Rev Biochem 1990 59:971-1005 |
| | |
| 8 | PKA
Pathway No. 135 | cAMP_pathway
Accession No. 25 | Network | Molecule = 9
Enzyme = 0
Reaction = 7
| Molecule = 0
Enzyme = 0
Reaction = 0
| Bhalla US Methods Enzymol. 2002;345:3-23). ( peer-reviewed publication )/
2002-01-12 00:00:00 |
| | #14Related Pathway:
17, 30, 84, 196, 220, 240, 250, 270, 277, 288, 326, 343, 361 |
| | General ref: Taylor et al Ann Rev Biochem 1990 59:971-1005 |
| | |
| 9 | PKA
Pathway No. 196 | PKA_2003
Accession No. 47 | Network | Molecule = 9
Enzyme = 0
Reaction = 7
| Molecule = 0
Enzyme = 0
Reaction = 0
| Bhalla US. (2004) Biophys J. 87(2):733-44. ( peer-reviewed publication )/
2003-04-28 00:00:00 |
| | #14Related Pathway:
17, 30, 84, 135, 220, 240, 250, 270, 277, 288, 326, 343, 361 |
| | General ref: Taylor et al Ann Rev Biochem 1990 59:971-1005 |
| | |
| 10 | PKA
Pathway No. 240 | AMPAR_traff_
model0
Accession No. 59 | Network | Molecule = 10
Enzyme = 35
Reaction = 7
| Molecule = 0
Enzyme = 1
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:
17, 30, 84, 135, 196, 220, 250, 270, 277, 288, 326, 343, 361 |
| | General ref: Taylor et al Ann Rev Biochem 1990 59:971-1005 |
| | 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. |
|
| 11 | PKA
Pathway No. 250 | AMPAR_traff_
model1
Accession No. 60 | Network | Molecule = 10
Enzyme = 35
Reaction = 7
| Molecule = 0
Enzyme = 1
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:
17, 30, 84, 135, 196, 220, 240, 270, 277, 288, 326, 343, 361 |
| | General ref: Taylor et al Ann Rev Biochem 1990 59:971-1005 |
| | 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. |
|
| 12 | PKA
Pathway No. 270 | CaMKII_model3
Accession No. 63 | Network | Molecule = 9
Enzyme = 0
Reaction = 7
| 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:
17, 30, 84, 135, 196, 220, 240, 250, 277, 288, 326, 343, 361 |
| | 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. |
|
| 13 | PKA
Pathway No. 277 | AMPAR_CaMKII_
strong_coupling
Accession No. 64 | Network | Molecule = 9
Enzyme = 0
Reaction = 7
| 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:
17, 30, 84, 135, 196, 220, 240, 250, 270, 288, 326, 343, 361 |
| | General ref: Taylor et al Ann Rev Biochem 1990 59:971-1005 |
| | 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. |
|
| 14 | PKA
Pathway No. 288 | AMPAR_CaMKII_
weak_coupling
Accession No. 65 | Network | Molecule = 10
Enzyme = 35
Reaction = 7
| Molecule = 0
Enzyme = 1
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:
17, 30, 84, 135, 196, 220, 240, 250, 270, 277, 326, 343, 361 |
| | General ref: Taylor et al Ann Rev Biochem 1990 59:971-1005 |
| | 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. |
|
or Pathway 