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Pathway List for cam | Default ordering is done according to Pathway Name.Table header can be used for changing the default ordering. indicates that ordering is done according to ascending or descending order. Entries are color tagged depending on Network or Pathway |
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Pathway Name Pathway No. | Accession Name Accession No. | Accession Type | Pathway statistics | cam statistics | Source Entry Date | 1 | CaM Pathway No. 14 | fig3_CaMKII
Accession No. 2 | Network | Molecule = 4 Enzyme = 0 Reaction = 5
| 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 | | #137Related Pathway: 27, 81, 107, 122, 146, 160, 173, 203, 217, 236, 246, 259, 265, 273, 283, 323, 340, 358, 368, 373, 379, 386, 392 398, 405, 411, 418, 423, 428, 434, 440, 446, 452, 458, 464, 470, 476, 482, 488, 494, 500, 506, 512, 518, 524, 530, 537 543, 549, 555, 561, 568, 573, 579, 585, 591, 597, 603, 609, 615, 621, 627, 633, 639, 645, 651, 657, 663, 669, 675, 681 688, 695, 701, 706, 712, 718, 724, 730, 736, 742, 748, 754, 760, 766, 772, 778, 784, 790, 796, 802, 808, 814, 820, 826 832, 838, 844, 850, 856, 862, 868, 874, 880, 886, 892, 898, 904, 910, 916, 924, 930, 936, 942, 948, 954, 961, 967, 973 979, 985, 991, 997, 1002, 1008, 1014, 1021, 1026, 1032, 1038, 1044, 1050, 1056, 1062, 1068, 1094 | | 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 | CaM Pathway No. 27 | fig4_synapse
Accession No. 3 | Network | Molecule = 4 Enzyme = 0 Reaction = 5
| 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 | | #137Related Pathway: 14, 81, 107, 122, 146, 160, 173, 203, 217, 236, 246, 259, 265, 273, 283, 323, 340, 358, 368, 373, 379, 386, 392 398, 405, 411, 418, 423, 428, 434, 440, 446, 452, 458, 464, 470, 476, 482, 488, 494, 500, 506, 512, 518, 524, 530, 537 543, 549, 555, 561, 568, 573, 579, 585, 591, 597, 603, 609, 615, 621, 627, 633, 639, 645, 651, 657, 663, 669, 675, 681 688, 695, 701, 706, 712, 718, 724, 730, 736, 742, 748, 754, 760, 766, 772, 778, 784, 790, 796, 802, 808, 814, 820, 826 832, 838, 844, 850, 856, 862, 868, 874, 880, 886, 892, 898, 904, 910, 916, 924, 930, 936, 942, 948, 954, 961, 967, 973 979, 985, 991, 997, 1002, 1008, 1014, 1021, 1026, 1032, 1038, 1044, 1050, 1056, 1062, 1068, 1094 | | 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 | CaM Pathway No. 81 | Synaptic_ Network Accession No. 16 | Network | Molecule = 4 Enzyme = 0 Reaction = 5
| Molecule = 1 Enzyme = 0 Reaction = 0
| Bhalla US and Iyengar R. Science (1999) 283(5400):381-7. ( peer-reviewed publication )/ 2001-12-12 00:00:00 | | #137Related Pathway: 14, 27, 107, 122, 146, 160, 173, 203, 217, 236, 246, 259, 265, 273, 283, 323, 340, 358, 368, 373, 379, 386, 392 398, 405, 411, 418, 423, 428, 434, 440, 446, 452, 458, 464, 470, 476, 482, 488, 494, 500, 506, 512, 518, 524, 530, 537 543, 549, 555, 561, 568, 573, 579, 585, 591, 597, 603, 609, 615, 621, 627, 633, 639, 645, 651, 657, 663, 669, 675, 681 688, 695, 701, 706, 712, 718, 724, 730, 736, 742, 748, 754, 760, 766, 772, 778, 784, 790, 796, 802, 808, 814, 820, 826 832, 838, 844, 850, 856, 862, 868, 874, 880, 886, 892, 898, 904, 910, 916, 924, 930, 936, 942, 948, 954, 961, 967, 973 979, 985, 991, 997, 1002, 1008, 1014, 1021, 1026, 1032, 1038, 1044, 1050, 1056, 1062, 1068, 1094 | | This is the basic Ca-binding-to-CaM model with the addition of neurogranin as a CaM se
questering molecule. Main data sources are Forsen et al 1986 Calcium and Cell funciton VI 113_
157 Drabikowski and Brzeska 1982 JBC 257(19):11584-11590 Martin et al 1985 Eur J Biochem 151(3)
:543-550 Stemmer and Klee 1994 Biochem 33:6859-6866 Data is pretty thorough. The Neurogranin in
fo is from several sources esp Huang et al 1993 ABB 305(2):570-580 Gerendasy et al 1994 JBC 269
(35) 22420-22426 is not very quantitative | | 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 |
| 4 | CaM Pathway No. 107 | NonOsc_Ca_ IP3metabolism Accession No. 23 | Network | Molecule = 4 Enzyme = 0 Reaction = 3
| Molecule = 1 Enzyme = 0 Reaction = 0
| Mishra J, Bhalla US. Biophys J. 2002 Sep;83(3):1298-316. ( peer-reviewed publication )/ 2002-01-07 00:00:00 | | #137Related Pathway: 14, 27, 81, 122, 146, 160, 173, 203, 217, 236, 246, 259, 265, 273, 283, 323, 340, 358, 368, 373, 379, 386, 392, 398 405, 411, 418, 423, 428, 434, 440, 446, 452, 458, 464, 470, 476, 482, 488, 494, 500, 506, 512, 518, 524, 530, 537, 543 549, 555, 561, 568, 573, 579, 585, 591, 597, 603, 609, 615, 621, 627, 633, 639, 645, 651, 657, 663, 669, 675, 681, 688 695, 701, 706, 712, 718, 724, 730, 736, 742, 748, 754, 760, 766, 772, 778, 784, 790, 796, 802, 808, 814, 820, 826, 832 838, 844, 850, 856, 862, 868, 874, 880, 886, 892, 898, 904, 910, 916, 924, 930, 936, 942, 948, 954, 961, 967, 973, 979 985, 991, 997, 1002, 1008, 1014, 1021, 1026, 1032, 1038, 1044, 1050, 1056, 1062, 1068, 1094 | | This is the basic Ca-binding-to-CaM model. Main data sources are Forsen S.et al (1986) in Calcium and Cell function, volume 6 (Cheung, W. Y., ed.) pp.112-157, Academic Press, New York and Drabikowski W. et al, J Biol Chem. 1982 Oct 10;257(19):11584-90 and Martin SR et al Eur J Biochem. 1985 Sep 16;151(3):543-50 and Stemmer PM, Klee CB Biochemistry. 1994 Jun 7;33(22):6859-66 Data is pretty thorough. | | 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 |
| 5 | CaM Pathway No. 122 | Osc_Ca_ IP3metabolism Accession No. 24 | Network | Molecule = 4 Enzyme = 0 Reaction = 3
| Molecule = 1 Enzyme = 0 Reaction = 0
| Mishra J, Bhalla US. Biophys J. 2002 Sep;83(3):1298-316. ( peer-reviewed publication )/ 2002-01-08 00:00:00 | | #137Related Pathway: 14, 27, 81, 107, 146, 160, 173, 203, 217, 236, 246, 259, 265, 273, 283, 323, 340, 358, 368, 373, 379, 386, 392, 398 405, 411, 418, 423, 428, 434, 440, 446, 452, 458, 464, 470, 476, 482, 488, 494, 500, 506, 512, 518, 524, 530, 537, 543 549, 555, 561, 568, 573, 579, 585, 591, 597, 603, 609, 615, 621, 627, 633, 639, 645, 651, 657, 663, 669, 675, 681, 688 695, 701, 706, 712, 718, 724, 730, 736, 742, 748, 754, 760, 766, 772, 778, 784, 790, 796, 802, 808, 814, 820, 826, 832 838, 844, 850, 856, 862, 868, 874, 880, 886, 892, 898, 904, 910, 916, 924, 930, 936, 942, 948, 954, 961, 967, 973, 979 985, 991, 997, 1002, 1008, 1014, 1021, 1026, 1032, 1038, 1044, 1050, 1056, 1062, 1068, 1094 | | This is the basic Ca-binding-to-CaM model. Main data sources are Forsen et al 1986 Calcium and Cell funciton VI 113_157 Drabikowski and Brzeska 1982 JBC 257(19):11584-11590 Martin et al 1985 Eur J Biochem 151(3):543-550 Stemmer and Klee 1994 Biochem 33:6859-6866 Data is pretty thorough. | | 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 |
| 6 | CaM Pathway No. 146 | NonOsc_Ca_ IP3metabolism Accession No. 31 | Network | Molecule = 4 Enzyme = 0 Reaction = 3
| Molecule = 1 Enzyme = 0 Reaction = 0
| Mishra J, Bhalla US. Biophys J. 2002 Sep;83(3):1298-316. ( peer-reviewed publication )/ 2002-04-03 00:00:00 | | #137Related Pathway: 14, 27, 81, 107, 122, 160, 173, 203, 217, 236, 246, 259, 265, 273, 283, 323, 340, 358, 368, 373, 379, 386, 392, 398 405, 411, 418, 423, 428, 434, 440, 446, 452, 458, 464, 470, 476, 482, 488, 494, 500, 506, 512, 518, 524, 530, 537, 543 549, 555, 561, 568, 573, 579, 585, 591, 597, 603, 609, 615, 621, 627, 633, 639, 645, 651, 657, 663, 669, 675, 681, 688 695, 701, 706, 712, 718, 724, 730, 736, 742, 748, 754, 760, 766, 772, 778, 784, 790, 796, 802, 808, 814, 820, 826, 832 838, 844, 850, 856, 862, 868, 874, 880, 886, 892, 898, 904, 910, 916, 924, 930, 936, 942, 948, 954, 961, 967, 973, 979 985, 991, 997, 1002, 1008, 1014, 1021, 1026, 1032, 1038, 1044, 1050, 1056, 1062, 1068, 1094 | | This is the basic Ca-binding-to-CaM model. Main data sources are Forsen et al 1986 Calcium and Cell funciton VI 113_157 Drabikowski and Brzeska 1982 JBC 257(19):11584-11590 Martin et al 1985 Eur J Biochem 151(3):543-550 Stemmer and Klee 1994 Biochem 33:6859-6866 Data is pretty thorough. | | 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 |
| 7 | CaM Pathway No. 160 | Osc_Ca_ IP3metabolism Accession No. 32 | Network | Molecule = 4 Enzyme = 0 Reaction = 3
| Molecule = 1 Enzyme = 0 Reaction = 0
| Mishra J, Bhalla US. Biophys J. 2002 Sep;83(3):1298-316. ( peer-reviewed publication )/ 2002-04-03 00:00:00 | | #137Related Pathway: 14, 27, 81, 107, 122, 146, 173, 203, 217, 236, 246, 259, 265, 273, 283, 323, 340, 358, 368, 373, 379, 386, 392, 398 405, 411, 418, 423, 428, 434, 440, 446, 452, 458, 464, 470, 476, 482, 488, 494, 500, 506, 512, 518, 524, 530, 537, 543 549, 555, 561, 568, 573, 579, 585, 591, 597, 603, 609, 615, 621, 627, 633, 639, 645, 651, 657, 663, 669, 675, 681, 688 695, 701, 706, 712, 718, 724, 730, 736, 742, 748, 754, 760, 766, 772, 778, 784, 790, 796, 802, 808, 814, 820, 826, 832 838, 844, 850, 856, 862, 868, 874, 880, 886, 892, 898, 904, 910, 916, 924, 930, 936, 942, 948, 954, 961, 967, 973, 979 985, 991, 997, 1002, 1008, 1014, 1021, 1026, 1032, 1038, 1044, 1050, 1056, 1062, 1068, 1094 | | This is the basic Ca-binding-to-CaM model. Main data sources are Forsen et al 1986 Calcium and Cell funciton VI 113_157 Drabikowski and Brzeska 1982 JBC 257(19):11584-11590 Martin et al 1985 Eur J Biochem 151(3):543-550 Stemmer and Klee 1994 Biochem 33:6859-6866 Data is pretty thorough. | | 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 |
| 8 | CaM Pathway No. 173 | CaMKII
Accession No. 33 | Network | Molecule = 5 Enzyme = 0 Reaction = 4
| Molecule = 1 Enzyme = 0 Reaction = 0
| William R. Holmes J Comput Neurosci. (2000) 8(1):65-85 ( peer-reviewed publication )/ 2002-08-21 00:00:00 | | #137Related Pathway: 14, 27, 81, 107, 122, 146, 160, 203, 217, 236, 246, 259, 265, 273, 283, 323, 340, 358, 368, 373, 379, 386, 392, 398 405, 411, 418, 423, 428, 434, 440, 446, 452, 458, 464, 470, 476, 482, 488, 494, 500, 506, 512, 518, 524, 530, 537, 543 549, 555, 561, 568, 573, 579, 585, 591, 597, 603, 609, 615, 621, 627, 633, 639, 645, 651, 657, 663, 669, 675, 681, 688 695, 701, 706, 712, 718, 724, 730, 736, 742, 748, 754, 760, 766, 772, 778, 784, 790, 796, 802, 808, 814, 820, 826, 832 838, 844, 850, 856, 862, 868, 874, 880, 886, 892, 898, 904, 910, 916, 924, 930, 936, 942, 948, 954, 961, 967, 973, 979 985, 991, 997, 1002, 1008, 1014, 1021, 1026, 1032, 1038, 1044, 1050, 1056, 1062, 1068, 1094 | | 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. | | | 9 | CaM Pathway No. 203 | CaMKII_2003
Accession No. 49 | Network | Molecule = 4 Enzyme = 0 Reaction = 5
| Molecule = 1 Enzyme = 0 Reaction = 0
| Bhalla US. Biophys J. 2004 Aug;87(2):733-44. ( peer-reviewed publication )./ 2003-04-28 00:00:00 | | #137Related Pathway: 14, 27, 81, 107, 122, 146, 160, 173, 217, 236, 246, 259, 265, 273, 283, 323, 340, 358, 368, 373, 379, 386, 392, 398 405, 411, 418, 423, 428, 434, 440, 446, 452, 458, 464, 470, 476, 482, 488, 494, 500, 506, 512, 518, 524, 530, 537, 543 549, 555, 561, 568, 573, 579, 585, 591, 597, 603, 609, 615, 621, 627, 633, 639, 645, 651, 657, 663, 669, 675, 681, 688 695, 701, 706, 712, 718, 724, 730, 736, 742, 748, 754, 760, 766, 772, 778, 784, 790, 796, 802, 808, 814, 820, 826, 832 838, 844, 850, 856, 862, 868, 874, 880, 886, 892, 898, 904, 910, 916, 924, 930, 936, 942, 948, 954, 961, 967, 973, 979 985, 991, 997, 1002, 1008, 1014, 1021, 1026, 1032, 1038, 1044, 1050, 1056, 1062, 1068, 1094 | | 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. |
| 10 | CaM Pathway No. 217 | MAPK_network_ 2003 Accession No. 50 | Network | Molecule = 4 Enzyme = 0 Reaction = 5
| Molecule = 1 Enzyme = 0 Reaction = 0
| Bhalla US Biophys J. 2004 Aug;87(2):745-53. ( peer-reviewed publication )/ 2003-04-28 00:00:00 | | #137Related Pathway: 14, 27, 81, 107, 122, 146, 160, 173, 203, 236, 246, 259, 265, 273, 283, 323, 340, 358, 368, 373, 379, 386, 392, 398 405, 411, 418, 423, 428, 434, 440, 446, 452, 458, 464, 470, 476, 482, 488, 494, 500, 506, 512, 518, 524, 530, 537, 543 549, 555, 561, 568, 573, 579, 585, 591, 597, 603, 609, 615, 621, 627, 633, 639, 645, 651, 657, 663, 669, 675, 681, 688 695, 701, 706, 712, 718, 724, 730, 736, 742, 748, 754, 760, 766, 772, 778, 784, 790, 796, 802, 808, 814, 820, 826, 832 838, 844, 850, 856, 862, 868, 874, 880, 886, 892, 898, 904, 910, 916, 924, 930, 936, 942, 948, 954, 961, 967, 973, 979 985, 991, 997, 1002, 1008, 1014, 1021, 1026, 1032, 1038, 1044, 1050, 1056, 1062, 1068, 1094 | | 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 | CaM Pathway No. 236 | AMPAR_traff_ model0 Accession No. 59 | Network | Molecule = 14 Enzyme = 0 Reaction = 11
| Molecule = 1 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 | | #137Related Pathway: 14, 27, 81, 107, 122, 146, 160, 173, 203, 217, 246, 259, 265, 273, 283, 323, 340, 358, 368, 373, 379, 386, 392, 398 405, 411, 418, 423, 428, 434, 440, 446, 452, 458, 464, 470, 476, 482, 488, 494, 500, 506, 512, 518, 524, 530, 537, 543 549, 555, 561, 568, 573, 579, 585, 591, 597, 603, 609, 615, 621, 627, 633, 639, 645, 651, 657, 663, 669, 675, 681, 688 695, 701, 706, 712, 718, 724, 730, 736, 742, 748, 754, 760, 766, 772, 778, 784, 790, 796, 802, 808, 814, 820, 826, 832 838, 844, 850, 856, 862, 868, 874, 880, 886, 892, 898, 904, 910, 916, 924, 930, 936, 942, 948, 954, 961, 967, 973, 979 985, 991, 997, 1002, 1008, 1014, 1021, 1026, 1032, 1038, 1044, 1050, 1056, 1062, 1068, 1094 | | 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. |
| 12 | CaM Pathway No. 246 | AMPAR_traff_ model1 Accession No. 60 | Network | Molecule = 14 Enzyme = 0 Reaction = 11
| Molecule = 1 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 | | #137Related Pathway: 14, 27, 81, 107, 122, 146, 160, 173, 203, 217, 236, 259, 265, 273, 283, 323, 340, 358, 368, 373, 379, 386, 392, 398 405, 411, 418, 423, 428, 434, 440, 446, 452, 458, 464, 470, 476, 482, 488, 494, 500, 506, 512, 518, 524, 530, 537, 543 549, 555, 561, 568, 573, 579, 585, 591, 597, 603, 609, 615, 621, 627, 633, 639, 645, 651, 657, 663, 669, 675, 681, 688 695, 701, 706, 712, 718, 724, 730, 736, 742, 748, 754, 760, 766, 772, 778, 784, 790, 796, 802, 808, 814, 820, 826, 832 838, 844, 850, 856, 862, 868, 874, 880, 886, 892, 898, 904, 910, 916, 924, 930, 936, 942, 948, 954, 961, 967, 973, 979 985, 991, 997, 1002, 1008, 1014, 1021, 1026, 1032, 1038, 1044, 1050, 1056, 1062, 1068, 1094 | | 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. |
| 13 | CaM Pathway No. 259 | CaMKII_noPKA_ model3 Accession No. 62 | Network | Molecule = 2 Enzyme = 0 Reaction = 5
| Molecule = 1 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 | | #137Related Pathway: 14, 27, 81, 107, 122, 146, 160, 173, 203, 217, 236, 246, 265, 273, 283, 323, 340, 358, 368, 373, 379, 386, 392, 398 405, 411, 418, 423, 428, 434, 440, 446, 452, 458, 464, 470, 476, 482, 488, 494, 500, 506, 512, 518, 524, 530, 537, 543 549, 555, 561, 568, 573, 579, 585, 591, 597, 603, 609, 615, 621, 627, 633, 639, 645, 651, 657, 663, 669, 675, 681, 688 695, 701, 706, 712, 718, 724, 730, 736, 742, 748, 754, 760, 766, 772, 778, 784, 790, 796, 802, 808, 814, 820, 826, 832 838, 844, 850, 856, 862, 868, 874, 880, 886, 892, 898, 904, 910, 916, 924, 930, 936, 942, 948, 954, 961, 967, 973, 979 985, 991, 997, 1002, 1008, 1014, 1021, 1026, 1032, 1038, 1044, 1050, 1056, 1062, 1068, 1094 | | 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. |
| 14 | CaM Pathway No. 265 | CaMKII_model3
Accession No. 63 | Network | Molecule = 2 Enzyme = 0 Reaction = 5
| Molecule = 1 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 | | #137Related Pathway: 14, 27, 81, 107, 122, 146, 160, 173, 203, 217, 236, 246, 259, 273, 283, 323, 340, 358, 368, 373, 379, 386, 392, 398 405, 411, 418, 423, 428, 434, 440, 446, 452, 458, 464, 470, 476, 482, 488, 494, 500, 506, 512, 518, 524, 530, 537, 543 549, 555, 561, 568, 573, 579, 585, 591, 597, 603, 609, 615, 621, 627, 633, 639, 645, 651, 657, 663, 669, 675, 681, 688 695, 701, 706, 712, 718, 724, 730, 736, 742, 748, 754, 760, 766, 772, 778, 784, 790, 796, 802, 808, 814, 820, 826, 832 838, 844, 850, 856, 862, 868, 874, 880, 886, 892, 898, 904, 910, 916, 924, 930, 936, 942, 948, 954, 961, 967, 973, 979 985, 991, 997, 1002, 1008, 1014, 1021, 1026, 1032, 1038, 1044, 1050, 1056, 1062, 1068, 1094 | | 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. |
| 15 | CaM Pathway No. 273 | AMPAR_CaMKII_ strong_coupling Accession No. 64 | Network | Molecule = 8 Enzyme = 0 Reaction = 9
| Molecule = 1 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 | | #137Related Pathway: 14, 27, 81, 107, 122, 146, 160, 173, 203, 217, 236, 246, 259, 265, 283, 323, 340, 358, 368, 373, 379, 386, 392, 398 405, 411, 418, 423, 428, 434, 440, 446, 452, 458, 464, 470, 476, 482, 488, 494, 500, 506, 512, 518, 524, 530, 537, 543 549, 555, 561, 568, 573, 579, 585, 591, 597, 603, 609, 615, 621, 627, 633, 639, 645, 651, 657, 663, 669, 675, 681, 688 695, 701, 706, 712, 718, 724, 730, 736, 742, 748, 754, 760, 766, 772, 778, 784, 790, 796, 802, 808, 814, 820, 826, 832 838, 844, 850, 856, 862, 868, 874, 880, 886, 892, 898, 904, 910, 916, 924, 930, 936, 942, 948, 954, 961, 967, 973, 979 985, 991, 997, 1002, 1008, 1014, 1021, 1026, 1032, 1038, 1044, 1050, 1056, 1062, 1068, 1094 | | 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. |
| 16 | CaM Pathway No. 283 | AMPAR_CaMKII_ weak_coupling Accession No. 65 | Network | Molecule = 8 Enzyme = 0 Reaction = 9
| Molecule = 1 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 | | #137Related Pathway: 14, 27, 81, 107, 122, 146, 160, 173, 203, 217, 236, 246, 259, 265, 273, 323, 340, 358, 368, 373, 379, 386, 392, 398 405, 411, 418, 423, 428, 434, 440, 446, 452, 458, 464, 470, 476, 482, 488, 494, 500, 506, 512, 518, 524, 530, 537, 543 549, 555, 561, 568, 573, 579, 585, 591, 597, 603, 609, 615, 621, 627, 633, 639, 645, 651, 657, 663, 669, 675, 681, 688 695, 701, 706, 712, 718, 724, 730, 736, 742, 748, 754, 760, 766, 772, 778, 784, 790, 796, 802, 808, 814, 820, 826, 832 838, 844, 850, 856, 862, 868, 874, 880, 886, 892, 898, 904, 910, 916, 924, 930, 936, 942, 948, 954, 961, 967, 973, 979 985, 991, 997, 1002, 1008, 1014, 1021, 1026, 1032, 1038, 1044, 1050, 1056, 1062, 1068, 1094 | | 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. |
| 17 | CaM Pathway No. 323 | Ajay_Bhalla_ 2004_PKM_Tuning Accession No. 76 | Network | Molecule = 4 Enzyme = 0 Reaction = 5
| Molecule = 1 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 | | #137Related Pathway: 14, 27, 81, 107, 122, 146, 160, 173, 203, 217, 236, 246, 259, 265, 273, 283, 340, 358, 368, 373, 379, 386, 392, 398 405, 411, 418, 423, 428, 434, 440, 446, 452, 458, 464, 470, 476, 482, 488, 494, 500, 506, 512, 518, 524, 530, 537, 543 549, 555, 561, 568, 573, 579, 585, 591, 597, 603, 609, 615, 621, 627, 633, 639, 645, 651, 657, 663, 669, 675, 681, 688 695, 701, 706, 712, 718, 724, 730, 736, 742, 748, 754, 760, 766, 772, 778, 784, 790, 796, 802, 808, 814, 820, 826, 832 838, 844, 850, 856, 862, 868, 874, 880, 886, 892, 898, 904, 910, 916, 924, 930, 936, 942, 948, 954, 961, 967, 973, 979 985, 991, 997, 1002, 1008, 1014, 1021, 1026, 1032, 1038, 1044, 1050, 1056, 1062, 1068, 1094 | | 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. |
| 18 | CaM Pathway No. 340 | Ajay_Bhalla_ 2004_PKM_MKP3_ Tuning Accession No. 77 | Network | Molecule = 4 Enzyme = 0 Reaction = 5
| Molecule = 1 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 | | #137Related Pathway: 14, 27, 81, 107, 122, 146, 160, 173, 203, 217, 236, 246, 259, 265, 273, 283, 323, 358, 368, 373, 379, 386, 392, 398 405, 411, 418, 423, 428, 434, 440, 446, 452, 458, 464, 470, 476, 482, 488, 494, 500, 506, 512, 518, 524, 530, 537, 543 549, 555, 561, 568, 573, 579, 585, 591, 597, 603, 609, 615, 621, 627, 633, 639, 645, 651, 657, 663, 669, 675, 681, 688 695, 701, 706, 712, 718, 724, 730, 736, 742, 748, 754, 760, 766, 772, 778, 784, 790, 796, 802, 808, 814, 820, 826, 832 838, 844, 850, 856, 862, 868, 874, 880, 886, 892, 898, 904, 910, 916, 924, 930, 936, 942, 948, 954, 961, 967, 973, 979 985, 991, 997, 1002, 1008, 1014, 1021, 1026, 1032, 1038, 1044, 1050, 1056, 1062, 1068, 1094 | | 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. |
| 19 | CaM Pathway No. 358 | Ajay_Bhalla_ 2004_Feedback_ Tuning Accession No. 78 | Network | Molecule = 4 Enzyme = 0 Reaction = 5
| Molecule = 1 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 | | #137Related Pathway: 14, 27, 81, 107, 122, 146, 160, 173, 203, 217, 236, 246, 259, 265, 273, 283, 323, 340, 368, 373, 379, 386, 392, 398 405, 411, 418, 423, 428, 434, 440, 446, 452, 458, 464, 470, 476, 482, 488, 494, 500, 506, 512, 518, 524, 530, 537, 543 549, 555, 561, 568, 573, 579, 585, 591, 597, 603, 609, 615, 621, 627, 633, 639, 645, 651, 657, 663, 669, 675, 681, 688 695, 701, 706, 712, 718, 724, 730, 736, 742, 748, 754, 760, 766, 772, 778, 784, 790, 796, 802, 808, 814, 820, 826, 832 838, 844, 850, 856, 862, 868, 874, 880, 886, 892, 898, 904, 910, 916, 924, 930, 936, 942, 948, 954, 961, 967, 973, 979 985, 991, 997, 1002, 1008, 1014, 1021, 1026, 1032, 1038, 1044, 1050, 1056, 1062, 1068, 1094 | | 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. |
| 20 | CaM Pathway No. 368 | Ajay_Bhalla_ 2007_Bistable Accession No. 79 | Network | Molecule = 4 Enzyme = 0 Reaction = 3
| Molecule = 1 Enzyme = 0 Reaction = 0
| Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87/ 2006-12-08 00:00:00 | | #137Related Pathway: 14, 27, 81, 107, 122, 146, 160, 173, 203, 217, 236, 246, 259, 265, 273, 283, 323, 340, 358, 373, 379, 386, 392, 398 405, 411, 418, 423, 428, 434, 440, 446, 452, 458, 464, 470, 476, 482, 488, 494, 500, 506, 512, 518, 524, 530, 537, 543 549, 555, 561, 568, 573, 579, 585, 591, 597, 603, 609, 615, 621, 627, 633, 639, 645, 651, 657, 663, 669, 675, 681, 688 695, 701, 706, 712, 718, 724, 730, 736, 742, 748, 754, 760, 766, 772, 778, 784, 790, 796, 802, 808, 814, 820, 826, 832 838, 844, 850, 856, 862, 868, 874, 880, 886, 892, 898, 904, 910, 916, 924, 930, 936, 942, 948, 954, 961, 967, 973, 979 985, 991, 997, 1002, 1008, 1014, 1021, 1026, 1032, 1038, 1044, 1050, 1056, 1062, 1068, 1094 | | This is a model of ERKII signaling which is bistable due to feedback. The feedback occurs through ERKII phosphorylation of phospholipase A2 (PLA2), leading to increased production of arachidonic acid (AA), which activates protein kinase C (PKC) which activates c-Raf which is upstream of ERKII. The model is a highly simplified variant of more detailed bistable models of MAPK signaling (Bhalla US, Iyengar R. Science. 1999 Jan 15;283(5400):381-7, Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80) | | This pathway is part of accession 79 and is completely specified in the file acc79.g. There is no separate files for just this pathway. |
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