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Pathway List for pkc Previous of 7  Next
Result: 1 - 20 of 135 rows are displayed
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 
  Pathway Name
Pathway No.		Accession Name
Accession No.		Accession
Type		Pathway statisticspkc statisticsSource
Entry Date
1 PKC
Pathway No. 138		 PKC_turnover

Accession No. 26		PathwayMolecule = 19
Enzyme   = 1
Reaction  = 17
Molecule = 0
Enzyme   = 0
Reaction  = 0
In-house /
2002-01-22 00:00:00
   Related Pathway: 
2, 20, 34, 55, 60, 71, 108, 123, 147, 161, 181, 200, 207, 313, 330, 348, 364, 370, 376, 383, 389, 395, 401, 408, 414
420, 426, 431, 437, 443, 449, 455, 461, 467, 473, 479, 485, 491, 497, 503, 509, 515, 521, 527, 534, 540, 546, 552, 558
564, 570, 576, 582, 588, 594, 600, 606, 612, 618, 624, 630, 636, 642, 648, 654, 660, 666, 672, 678, 685, 691, 698, 703
709, 715, 721, 727, 733, 739, 745, 751, 757, 763, 769, 775, 781, 787, 793, 799, 805, 811, 817, 823, 829, 835, 841, 847
853, 859, 865, 871, 877, 883, 889, 895, 901, 907, 913, 919, 927, 932, 938, 944, 950, 956, 963, 969, 974, 981, 987, 993
999, 1004, 1010, 1016, 1022, 1028, 1034, 1040, 1046, 1052, 1058, 1064, 1104
    This enzyme represents an averaged PKC activity, most closely based on the alpha, beta, and gamma forms.
   
This pathway is part of accession 26 and is completely specified in the file acc26.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc26.g   
GENESIS Format (Annotated version)    Anno_acc26.g   
MATLAB format    acc26.m   
SBML format    acc26.xml   
2 PKC
Pathway No. 200		 PKC_2003

Accession No. 48		PathwayMolecule = 11
Enzyme   = 0
Reaction  = 10
Molecule = 0
Enzyme   = 0
Reaction  = 0
Bhalla US. (2004) Biophys J. 87(2):733-44 .( peer-reviewed publication )/
2003-04-28 00:00:00
   Related Pathway: 
2, 20, 34, 55, 60, 71, 108, 123, 138, 147, 161, 181, 207, 313, 330, 348, 364, 370, 376, 383, 389, 395, 401, 408, 414
420, 426, 431, 437, 443, 449, 455, 461, 467, 473, 479, 485, 491, 497, 503, 509, 515, 521, 527, 534, 540, 546, 552, 558
564, 570, 576, 582, 588, 594, 600, 606, 612, 618, 624, 630, 636, 642, 648, 654, 660, 666, 672, 678, 685, 691, 698, 703
709, 715, 721, 727, 733, 739, 745, 751, 757, 763, 769, 775, 781, 787, 793, 799, 805, 811, 817, 823, 829, 835, 841, 847
853, 859, 865, 871, 877, 883, 889, 895, 901, 907, 913, 919, 927, 932, 938, 944, 950, 956, 963, 969, 974, 981, 987, 993
999, 1004, 1010, 1016, 1022, 1028, 1034, 1040, 1046, 1052, 1058, 1064, 1104
    This model consists of receptor-ligand interaction, G-protein activation, Adenylyl cyclase mediated formation of cAMP and activation of PKA in the neuron. Demonstration programs using this model described in Bhalla US. (2004) Biophys J. 87(2):733-44 to generate a dose-response curve using stochastic calculations are available here.
   
This pathway is part of accession 48 and is completely specified in the file acc48.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc48.g   
GENESIS Format (Annotated version)    Anno_acc48.g   
MATLAB format    acc48.m   
SBML format    acc48.xml   
3 PKC
Pathway No. 2		 fig2_egfr

Accession No. 1		NetworkMolecule = 11
Enzyme   = 0
Reaction  = 10
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
   Related Pathway: 
20, 34, 55, 60, 71, 108, 123, 138, 147, 161, 181, 200, 207, 313, 330, 348, 364, 370, 376, 383, 389, 395, 401, 408
414, 420, 426, 431, 437, 443, 449, 455, 461, 467, 473, 479, 485, 491, 497, 503, 509, 515, 521, 527, 534, 540, 546, 552
558, 564, 570, 576, 582, 588, 594, 600, 606, 612, 618, 624, 630, 636, 642, 648, 654, 660, 666, 672, 678, 685, 691, 698
703, 709, 715, 721, 727, 733, 739, 745, 751, 757, 763, 769, 775, 781, 787, 793, 799, 805, 811, 817, 823, 829, 835, 841
847, 853, 859, 865, 871, 877, 883, 889, 895, 901, 907, 913, 919, 927, 932, 938, 944, 950, 956, 963, 969, 974, 981, 987
993, 999, 1004, 1010, 1016, 1022, 1028, 1034, 1040, 1046, 1052, 1058, 1064, 1104
    This network was used to generate figure 2 in Bhalla US and Iyengar R. Science (1999) 283(5400):381-7. It consists of the MAPK cascade in a feedback loop with PKC, and receives input from the EGFR in the synapse.
Demonstration script files for generating the figures in the paper, including figure 2, are available here.
   
This pathway is part of accession 1 and is completely specified in the file acc1.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc1.g   
GENESIS Format (Annotated version)    Anno_acc1.g   
4 PKC
Pathway No. 20		 fig4_synapse

Accession No. 3		NetworkMolecule = 11
Enzyme   = 0
Reaction  = 10
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
   Related Pathway: 
2, 34, 55, 60, 71, 108, 123, 138, 147, 161, 181, 200, 207, 313, 330, 348, 364, 370, 376, 383, 389, 395, 401, 408, 414
420, 426, 431, 437, 443, 449, 455, 461, 467, 473, 479, 485, 491, 497, 503, 509, 515, 521, 527, 534, 540, 546, 552, 558
564, 570, 576, 582, 588, 594, 600, 606, 612, 618, 624, 630, 636, 642, 648, 654, 660, 666, 672, 678, 685, 691, 698, 703
709, 715, 721, 727, 733, 739, 745, 751, 757, 763, 769, 775, 781, 787, 793, 799, 805, 811, 817, 823, 829, 835, 841, 847
853, 859, 865, 871, 877, 883, 889, 895, 901, 907, 913, 919, 927, 932, 938, 944, 950, 956, 963, 969, 974, 981, 987, 993
999, 1004, 1010, 1016, 1022, 1028, 1034, 1040, 1046, 1052, 1058, 1064, 1104
    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.
FormatFile
Native Format (GENESIS format)    acc3.g   
GENESIS Format (Annotated version)    Anno_acc3.g   
5 PKC
Pathway No. 34		 mkp1_feedback_
effects
Accession No. 4		NetworkMolecule = 11
Enzyme   = 0
Reaction  = 10
Molecule = 0
Enzyme   = 0
Reaction  = 0
Bhalla US et al. Science (2002) 297(5583):1018-23. ( peer-reviewed publication )/
2001-11-07 00:00:00
   Related Pathway: 
2, 20, 55, 60, 71, 108, 123, 138, 147, 161, 181, 200, 207, 313, 330, 348, 364, 370, 376, 383, 389, 395, 401, 408, 414
420, 426, 431, 437, 443, 449, 455, 461, 467, 473, 479, 485, 491, 497, 503, 509, 515, 521, 527, 534, 540, 546, 552, 558
564, 570, 576, 582, 588, 594, 600, 606, 612, 618, 624, 630, 636, 642, 648, 654, 660, 666, 672, 678, 685, 691, 698, 703
709, 715, 721, 727, 733, 739, 745, 751, 757, 763, 769, 775, 781, 787, 793, 799, 805, 811, 817, 823, 829, 835, 841, 847
853, 859, 865, 871, 877, 883, 889, 895, 901, 907, 913, 919, 927, 932, 938, 944, 950, 956, 963, 969, 974, 981, 987, 993
999, 1004, 1010, 1016, 1022, 1028, 1034, 1040, 1046, 1052, 1058, 1064, 1104
    Protein Kinase C. This module represents a weighted average of the alpha, beta and gamma isoforms. It takes inputs from Ca, DAG (Diacyl Glycerol) and AA (arachidonic acid). Regulation parameters are largely from Schaechter and Benowitz 1993 J Neurosci 13(10):4361 who use synaptosomes from mammalian brain and in one paper look at all three inputs. Shinomura et al 1991 PNAS 88:5149-5153 is also a useful source of data and helps to tighten the DAG inputs. General reviews include Azzi et al 1992 Eur J Bioch 208:541 and Nishizuka 1988, Nature 334:661 Concentration info from Kikkawa et al 1982 JBC 257(22):13341 The process of parameterization is described in detail in several places. See Supplementary notes to Bhalla and Iyengar 1999 Science 284:92-96, available at the site http://www.ncbs.res.in/~bhalla/ltploop/pkc_example.html The parameterization is also described in a book chapter: Bhalla, 2000: Simulations of Biochemical Signaling in Computational Neuroscience: Realistic Modeling for Experimentalists. Ed. E. De Schutter. CRC Press.
   
This pathway is part of accession 4 and is completely specified in the file acc4.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc4.g   
GENESIS Format (Annotated version)    Anno_acc4.g   
MATLAB format    acc4.m   
SBML format    acc4.xml   
6 PKC
Pathway No. 55		 3d_fold_model

Accession No. 8		NetworkMolecule = 11
Enzyme   = 0
Reaction  = 10
Molecule = 0
Enzyme   = 0
Reaction  = 0
Bhalla US and Iyengar R. Science (1999) 283(5400):381-7. ( peer-reviewed publication )/
2001-11-08 00:00:00
   Related Pathway: 
2, 20, 34, 60, 71, 108, 123, 138, 147, 161, 181, 200, 207, 313, 330, 348, 364, 370, 376, 383, 389, 395, 401, 408, 414
420, 426, 431, 437, 443, 449, 455, 461, 467, 473, 479, 485, 491, 497, 503, 509, 515, 521, 527, 534, 540, 546, 552, 558
564, 570, 576, 582, 588, 594, 600, 606, 612, 618, 624, 630, 636, 642, 648, 654, 660, 666, 672, 678, 685, 691, 698, 703
709, 715, 721, 727, 733, 739, 745, 751, 757, 763, 769, 775, 781, 787, 793, 799, 805, 811, 817, 823, 829, 835, 841, 847
853, 859, 865, 871, 877, 883, 889, 895, 901, 907, 913, 919, 927, 932, 938, 944, 950, 956, 963, 969, 974, 981, 987, 993
999, 1004, 1010, 1016, 1022, 1028, 1034, 1040, 1046, 1052, 1058, 1064, 1104
    This model is an annotated version of the synaptic signaling network.
The primary reference is Bhalla US and Iyengar R. Science (1999) 283(5400):381-7 but several of the model pathways have been updated Bhalla US, Ram PT, Iyengar R. Science. 2002 Aug 9;297(5583):1018-23.
   
This pathway is part of accession 8 and is completely specified in the file acc8.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc8.g   
GENESIS Format (Annotated version)    Anno_acc8.g   
MATLAB format    acc8.m   
SBML format    acc8.xml   
7 PKC
Pathway No. 60		 MAPK_MKP1_
oscillation
Accession No. 9		NetworkMolecule = 11
Enzyme   = 0
Reaction  = 10
Molecule = 0
Enzyme   = 0
Reaction  = 0
Bhalla US, Iyengar R. Chaos (2001) 11(1):221-226. ( peer-reviewed publication )/
2001-11-08 00:00:00
   Related Pathway: 
2, 20, 34, 55, 71, 108, 123, 138, 147, 161, 181, 200, 207, 313, 330, 348, 364, 370, 376, 383, 389, 395, 401, 408, 414
420, 426, 431, 437, 443, 449, 455, 461, 467, 473, 479, 485, 491, 497, 503, 509, 515, 521, 527, 534, 540, 546, 552, 558
564, 570, 576, 582, 588, 594, 600, 606, 612, 618, 624, 630, 636, 642, 648, 654, 660, 666, 672, 678, 685, 691, 698, 703
709, 715, 721, 727, 733, 739, 745, 751, 757, 763, 769, 775, 781, 787, 793, 799, 805, 811, 817, 823, 829, 835, 841, 847
853, 859, 865, 871, 877, 883, 889, 895, 901, 907, 913, 919, 927, 932, 938, 944, 950, 956, 963, 969, 974, 981, 987, 993
999, 1004, 1010, 1016, 1022, 1028, 1034, 1040, 1046, 1052, 1058, 1064, 1104
    This model relates to figure 5 in Bhalla US, Iyengar R. Chaos (2001) 11(1):221-226. It includes the model used for figures 2-4 and also has MKP-1 induction by MAPK activity in the synapse. PP2A is set to 0.16 uM and MKP synthesis is varied from 5x to 40 x basal to get a range of interesting behaviours.
   
This pathway is part of accession 9 and is completely specified in the file acc9.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc9.g   
GENESIS Format (Annotated version)    Anno_acc9.g   
GENESIS Format (Annotated version)    Anno_acc9.g   
MATLAB format    acc9.m   
SBML format    acc9.xml   
8 PKC
Pathway No. 71		 Synaptic_
Network
Accession No. 16		NetworkMolecule = 11
Enzyme   = 0
Reaction  = 10
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
   Related Pathway: 
2, 20, 34, 55, 60, 108, 123, 138, 147, 161, 181, 200, 207, 313, 330, 348, 364, 370, 376, 383, 389, 395, 401, 408, 414
420, 426, 431, 437, 443, 449, 455, 461, 467, 473, 479, 485, 491, 497, 503, 509, 515, 521, 527, 534, 540, 546, 552, 558
564, 570, 576, 582, 588, 594, 600, 606, 612, 618, 624, 630, 636, 642, 648, 654, 660, 666, 672, 678, 685, 691, 698, 703
709, 715, 721, 727, 733, 739, 745, 751, 757, 763, 769, 775, 781, 787, 793, 799, 805, 811, 817, 823, 829, 835, 841, 847
853, 859, 865, 871, 877, 883, 889, 895, 901, 907, 913, 919, 927, 932, 938, 944, 950, 956, 963, 969, 974, 981, 987, 993
999, 1004, 1010, 1016, 1022, 1028, 1034, 1040, 1046, 1052, 1058, 1064, 1104
    Protein Kinase C. This module represents a weighted average of the alpha, beta and gamma isoforms. It takes inputs from Ca, DAG (Diacyl Glycerol) and AA (arachidonic acid). Regulation parameters are largely from Schaechter and Benowitz 1993 J Neurosci 13(10):4361 who use synaptosomes from mammalian brain and in one paper look at all three inputs. Shinomura et al 1991 PNAS 88:5149-5153 is also a useful source of data and helps to tighten the DAG inputs. General reviews include Azzi et al 1992 Eur J Bioch 208:541 and Nishizuka 1988, Nature 334:661 Concentration info from Kikkawa et al 1982 JBC 257(22):13341 The process of parameterization is described in detail in several places. See Supplementary notes to Bhalla and Iyengar 1999 Science 284:92-96, available at the site http://www.ncbs.res.in/~bhalla/ltploop/pkc_example.html The parameterization is also described in a book chapter: Bhalla, 2000: Simulations of Biochemical Signaling in Computational Neuroscience: Realistic Modeling for Experimentalists. Ed. E. De Schutter. CRC Press.
   
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.
FormatFile
Native Format (GENESIS format)    acc16.g   
GENESIS Format (Annotated version)    Anno_acc16.g   
9 PKC
Pathway No. 108		 NonOsc_Ca_
IP3metabolism
Accession No. 23		NetworkMolecule = 13
Enzyme   = 1
Reaction  = 10
Molecule = 0
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
   Related Pathway: 
2, 20, 34, 55, 60, 71, 123, 138, 147, 161, 181, 200, 207, 313, 330, 348, 364, 370, 376, 383, 389, 395, 401, 408, 414
420, 426, 431, 437, 443, 449, 455, 461, 467, 473, 479, 485, 491, 497, 503, 509, 515, 521, 527, 534, 540, 546, 552, 558
564, 570, 576, 582, 588, 594, 600, 606, 612, 618, 624, 630, 636, 642, 648, 654, 660, 666, 672, 678, 685, 691, 698, 703
709, 715, 721, 727, 733, 739, 745, 751, 757, 763, 769, 775, 781, 787, 793, 799, 805, 811, 817, 823, 829, 835, 841, 847
853, 859, 865, 871, 877, 883, 889, 895, 901, 907, 913, 919, 927, 932, 938, 944, 950, 956, 963, 969, 974, 981, 987, 993
999, 1004, 1010, 1016, 1022, 1028, 1034, 1040, 1046, 1052, 1058, 1064, 1104
    Protein Kinase C. This module represents a weighted average of the alpha, beta and gamma isoforms. It takes inputs from Ca, DAG (Diacyl Glycerol) and AA (arachidonic acid). Regulation parameters are largely from Schaechter JD, Benowitz LI J Neurosci. 1993 Oct;13(10):4361-71 who use synaptosomes from mammalian brain and in one paper look at all three inputs. Shinomura T et al Proc Natl Acad Sci U S A. 1991 Jun 15;88(12):5149-53 is also a useful source of data and helps to tighten the DAG inputs. General reviews include Azzi A et. al Eur J Biochem. 1992 Sep 15;208(3):547-57 and Nishizuka Y.Nature. 1988 Aug 25;334(6184):661-5. Concentration info from Kikkawa U.et al J Biol Chem. 1982 Nov 25;257(22):13341-8. The process of parameterization is described in detail in several places. See Supplementary notes to Weng G et al, Science. 1999 Apr 2;284(5411):92-6 available at the site http://www.ncbs.res.in/~bhalla/ltploop/ltploop/pkc_example.html. The parameterization is also described in a book chapter: Bhalla, 2000: Simulations of Biochemical Signaling in Computational Neuroscience: Realistic Modeling for Experimentalists. Ed. E. De Schutter. CRC Press.
   
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.
FormatFile
Native Format (GENESIS format)    acc23.g   
GENESIS Format (Annotated version)    Anno_acc23.g   
10 PKC
Pathway No. 123		 Osc_Ca_
IP3metabolism
Accession No. 24		NetworkMolecule = 13
Enzyme   = 1
Reaction  = 10
Molecule = 0
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
   Related Pathway: 
2, 20, 34, 55, 60, 71, 108, 138, 147, 161, 181, 200, 207, 313, 330, 348, 364, 370, 376, 383, 389, 395, 401, 408, 414
420, 426, 431, 437, 443, 449, 455, 461, 467, 473, 479, 485, 491, 497, 503, 509, 515, 521, 527, 534, 540, 546, 552, 558
564, 570, 576, 582, 588, 594, 600, 606, 612, 618, 624, 630, 636, 642, 648, 654, 660, 666, 672, 678, 685, 691, 698, 703
709, 715, 721, 727, 733, 739, 745, 751, 757, 763, 769, 775, 781, 787, 793, 799, 805, 811, 817, 823, 829, 835, 841, 847
853, 859, 865, 871, 877, 883, 889, 895, 901, 907, 913, 919, 927, 932, 938, 944, 950, 956, 963, 969, 974, 981, 987, 993
999, 1004, 1010, 1016, 1022, 1028, 1034, 1040, 1046, 1052, 1058, 1064, 1104
    Protein Kinase C. This module represents a weighted average of the alpha, beta and gamma isoforms. It takes inputs from Ca, DAG (Diacyl Glycerol) and AA (arachidonic acid). Regulation parameters are largely from Schaechter and Benowitz 1993 J Neurosci 13(10):4361 who use synaptosomes from mammalian brain and in one paper look at all three inputs. Shinomura et al 1991 PNAS 88:5149-5153 is also a useful source of data and helps to tighten the DAG inputs. General reviews include Azzi et al 1992 Eur J Bioch 208:541 and Nishizuka 1988, Nature 334:661 Concentration info from Kikkawa et al 1982 JBC 257(22):13341 The process of parameterization is described in detail in several places. See Supplementary notes to Bhalla and Iyengar 1999 Science 284:92-96, available at the site http://www.ncbs.res.in/~bhalla/ltploop/pkc_example.html The parameterization is also described in a book chapter: Bhalla, 2000: Simulations of Biochemical Signaling in Computational Neuroscience: Realistic Modeling for Experimentalists. Ed. E. De Schutter. CRC Press.
   
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.
FormatFile
Native Format (GENESIS format)    acc24.g   
GENESIS Format (Annotated version)    Anno_acc24.g   
11 PKC
Pathway No. 147		 NonOsc_Ca_
IP3metabolism
Accession No. 31		NetworkMolecule = 13
Enzyme   = 1
Reaction  = 10
Molecule = 0
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
   Related Pathway: 
2, 20, 34, 55, 60, 71, 108, 123, 138, 161, 181, 200, 207, 313, 330, 348, 364, 370, 376, 383, 389, 395, 401, 408, 414
420, 426, 431, 437, 443, 449, 455, 461, 467, 473, 479, 485, 491, 497, 503, 509, 515, 521, 527, 534, 540, 546, 552, 558
564, 570, 576, 582, 588, 594, 600, 606, 612, 618, 624, 630, 636, 642, 648, 654, 660, 666, 672, 678, 685, 691, 698, 703
709, 715, 721, 727, 733, 739, 745, 751, 757, 763, 769, 775, 781, 787, 793, 799, 805, 811, 817, 823, 829, 835, 841, 847
853, 859, 865, 871, 877, 883, 889, 895, 901, 907, 913, 919, 927, 932, 938, 944, 950, 956, 963, 969, 974, 981, 987, 993
999, 1004, 1010, 1016, 1022, 1028, 1034, 1040, 1046, 1052, 1058, 1064, 1104
    Protein Kinase C. This module represents a weighted average of the alpha, beta and gamma isoforms. It takes inputs from Ca, DAG (Diacyl Glycerol) and AA (arachidonic acid). Regulation parameters are largely from Schaechter and Benowitz 1993 J Neurosci 13(10):4361 who use synaptosomes from mammalian brain and in one paper look at all three inputs. Shinomura et al 1991 PNAS 88:5149-5153 is also a useful source of data and helps to tighten the DAG inputs. General reviews include Azzi et al 1992 Eur J Bioch 208:541 and Nishizuka 1988, Nature 334:661 Concentration info from Kikkawa et al 1982 JBC 257(22):13341 The process of parameterization is described in detail in several places. See Supplementary notes to Bhalla and Iyengar 1999 Science 284:92-96, available at the site http://www.ncbs.res.in/~bhalla/ltploop/pkc_example.html The parameterization is also described in a book chapter: Bhalla, 2000: Simulations of Biochemical Signaling in Computational Neuroscience: Realistic Modeling for Experimentalists. Ed. E. De Schutter. CRC Press.
   
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.
FormatFile
Native Format (GENESIS format)    acc31.g   
GENESIS Format (Annotated version)    Anno_acc31.g   
12 PKC
Pathway No. 161		 Osc_Ca_
IP3metabolism
Accession No. 32		NetworkMolecule = 13
Enzyme   = 1
Reaction  = 10
Molecule = 0
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
   Related Pathway: 
2, 20, 34, 55, 60, 71, 108, 123, 138, 147, 181, 200, 207, 313, 330, 348, 364, 370, 376, 383, 389, 395, 401, 408, 414
420, 426, 431, 437, 443, 449, 455, 461, 467, 473, 479, 485, 491, 497, 503, 509, 515, 521, 527, 534, 540, 546, 552, 558
564, 570, 576, 582, 588, 594, 600, 606, 612, 618, 624, 630, 636, 642, 648, 654, 660, 666, 672, 678, 685, 691, 698, 703
709, 715, 721, 727, 733, 739, 745, 751, 757, 763, 769, 775, 781, 787, 793, 799, 805, 811, 817, 823, 829, 835, 841, 847
853, 859, 865, 871, 877, 883, 889, 895, 901, 907, 913, 919, 927, 932, 938, 944, 950, 956, 963, 969, 974, 981, 987, 993
999, 1004, 1010, 1016, 1022, 1028, 1034, 1040, 1046, 1052, 1058, 1064, 1104
    Protein Kinase C. This module represents a weighted average of the alpha, beta and gamma isoforms. It takes inputs from Ca, DAG (Diacyl Glycerol) and AA (arachidonic acid). Regulation parameters are largely from Schaechter and Benowitz 1993 J Neurosci 13(10):4361 who use synaptosomes from mammalian brain and in one paper look at all three inputs. Shinomura et al 1991 PNAS 88:5149-5153 is also a useful source of data and helps to tighten the DAG inputs. General reviews include Azzi et al 1992 Eur J Bioch 208:541 and Nishizuka 1988, Nature 334:661 Concentration info from Kikkawa et al 1982 JBC 257(22):13341 The process of parameterization is described in detail in several places. See Supplementary notes to Bhalla and Iyengar 1999 Science 284:92-96, available at the site http://www.ncbs.res.in/~bhalla/ltploop/pkc_example.html The parameterization is also described in a book chapter: Bhalla, 2000: Simulations of Biochemical Signaling in Computational Neuroscience: Realistic Modeling for Experimentalists. Ed. E. De Schutter. CRC Press.
   
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.
FormatFile
Native Format (GENESIS format)    acc32.g   
GENESIS Format (Annotated version)    Anno_acc32.g   
13 PKC
Pathway No. 181		 MAPK-bistability
-fig1c
Accession No. 35		NetworkMolecule = 11
Enzyme   = 0
Reaction  = 10
Molecule = 0
Enzyme   = 0
Reaction  = 0
Bhalla US et al. Science (2002) 297(5583):1018-23 ( peer-reviewed publication )./
2002-11-07 00:00:00
   Related Pathway: 
2, 20, 34, 55, 60, 71, 108, 123, 138, 147, 161, 200, 207, 313, 330, 348, 364, 370, 376, 383, 389, 395, 401, 408, 414
420, 426, 431, 437, 443, 449, 455, 461, 467, 473, 479, 485, 491, 497, 503, 509, 515, 521, 527, 534, 540, 546, 552, 558
564, 570, 576, 582, 588, 594, 600, 606, 612, 618, 624, 630, 636, 642, 648, 654, 660, 666, 672, 678, 685, 691, 698, 703
709, 715, 721, 727, 733, 739, 745, 751, 757, 763, 769, 775, 781, 787, 793, 799, 805, 811, 817, 823, 829, 835, 841, 847
853, 859, 865, 871, 877, 883, 889, 895, 901, 907, 913, 919, 927, 932, 938, 944, 950, 956, 963, 969, 974, 981, 987, 993
999, 1004, 1010, 1016, 1022, 1028, 1034, 1040, 1046, 1052, 1058, 1064, 1104
    Protein Kinase C. This module represents a weighted average of the alpha, beta and gamma isoforms. It takes inputs from Ca, DAG (Diacyl Glycerol) and AA (arachidonic acid). Regulation parameters are largely from Schaechter and Benowitz 1993 J Neurosci 13(10):4361 who use synaptosomes from mammalian brain and in one paper look at all three inputs. Shinomura et al 1991 PNAS 88:5149-5153 is also a useful source of data and helps to tighten the DAG inputs. General reviews include Azzi et al 1992 Eur J Bioch 208:541 and Nishizuka 1988, Nature 334:661 Concentration info from Kikkawa et al 1982 JBC 257(22):13341 The process of parameterization is described in detail in several places. See Supplementary notes to Bhalla and Iyengar 1999 Science 284:92-96, available at the site http://www.ncbs.res.in/~bhalla/ltploop/pkc_example.html The parameterization is also described in a book chapter: Bhalla, 2000: Simulations of Biochemical Signaling in Computational Neuroscience: Realistic Modeling for Experimentalists. Ed. E. De Schutter. CRC Press.
   
This pathway is part of accession 35 and is completely specified in the file acc35.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc35.g   
GENESIS Format (Annotated version)    Anno_acc35.g   
MATLAB format    acc35.m   
SBML format    acc35.xml   
14 PKC
Pathway No. 207		 MAPK_network_
2003
Accession No. 50		NetworkMolecule = 11
Enzyme   = 0
Reaction  = 10
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
   Related Pathway: 
2, 20, 34, 55, 60, 71, 108, 123, 138, 147, 161, 181, 200, 313, 330, 348, 364, 370, 376, 383, 389, 395, 401, 408, 414
420, 426, 431, 437, 443, 449, 455, 461, 467, 473, 479, 485, 491, 497, 503, 509, 515, 521, 527, 534, 540, 546, 552, 558
564, 570, 576, 582, 588, 594, 600, 606, 612, 618, 624, 630, 636, 642, 648, 654, 660, 666, 672, 678, 685, 691, 698, 703
709, 715, 721, 727, 733, 739, 745, 751, 757, 763, 769, 775, 781, 787, 793, 799, 805, 811, 817, 823, 829, 835, 841, 847
853, 859, 865, 871, 877, 883, 889, 895, 901, 907, 913, 919, 927, 932, 938, 944, 950, 956, 963, 969, 974, 981, 987, 993
999, 1004, 1010, 1016, 1022, 1028, 1034, 1040, 1046, 1052, 1058, 1064, 1104
    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
   
FormatFile
Native Format (GENESIS format)    path207.g   
GENESIS Format (Annotated version)    Anno_path207.g   
MATLAB format    path207.m   
15 PKC
Pathway No. 313		 Ajay_Bhalla_
2004_PKM_Tuning
Accession No. 76		NetworkMolecule = 7
Enzyme   = 0
Reaction  = 5
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
   Related Pathway: 
2, 20, 34, 55, 60, 71, 108, 123, 138, 147, 161, 181, 200, 207, 330, 348, 364, 370, 376, 383, 389, 395, 401, 408, 414
420, 426, 431, 437, 443, 449, 455, 461, 467, 473, 479, 485, 491, 497, 503, 509, 515, 521, 527, 534, 540, 546, 552, 558
564, 570, 576, 582, 588, 594, 600, 606, 612, 618, 624, 630, 636, 642, 648, 654, 660, 666, 672, 678, 685, 691, 698, 703
709, 715, 721, 727, 733, 739, 745, 751, 757, 763, 769, 775, 781, 787, 793, 799, 805, 811, 817, 823, 829, 835, 841, 847
853, 859, 865, 871, 877, 883, 889, 895, 901, 907, 913, 919, 927, 932, 938, 944, 950, 956, 963, 969, 974, 981, 987, 993
999, 1004, 1010, 1016, 1022, 1028, 1034, 1040, 1046, 1052, 1058, 1064, 1104
    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.
FormatFile
Native Format (GENESIS format)    acc76.g   
MATLAB format    acc76.m   
SBML format    acc76.xml   
16 PKC
Pathway No. 330		 Ajay_Bhalla_
2004_PKM_MKP3_
Tuning
Accession No. 77		NetworkMolecule = 7
Enzyme   = 0
Reaction  = 5
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
   Related Pathway: 
2, 20, 34, 55, 60, 71, 108, 123, 138, 147, 161, 181, 200, 207, 313, 348, 364, 370, 376, 383, 389, 395, 401, 408, 414
420, 426, 431, 437, 443, 449, 455, 461, 467, 473, 479, 485, 491, 497, 503, 509, 515, 521, 527, 534, 540, 546, 552, 558
564, 570, 576, 582, 588, 594, 600, 606, 612, 618, 624, 630, 636, 642, 648, 654, 660, 666, 672, 678, 685, 691, 698, 703
709, 715, 721, 727, 733, 739, 745, 751, 757, 763, 769, 775, 781, 787, 793, 799, 805, 811, 817, 823, 829, 835, 841, 847
853, 859, 865, 871, 877, 883, 889, 895, 901, 907, 913, 919, 927, 932, 938, 944, 950, 956, 963, 969, 974, 981, 987, 993
999, 1004, 1010, 1016, 1022, 1028, 1034, 1040, 1046, 1052, 1058, 1064, 1104
    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.
FormatFile
Native Format (GENESIS format)    acc77.g   
MATLAB format    acc77.m   
SBML format    acc77.xml   
17 PKC
Pathway No. 348		 Ajay_Bhalla_
2004_Feedback_
Tuning
Accession No. 78		NetworkMolecule = 11
Enzyme   = 0
Reaction  = 10
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
   Related Pathway: 
2, 20, 34, 55, 60, 71, 108, 123, 138, 147, 161, 181, 200, 207, 313, 330, 364, 370, 376, 383, 389, 395, 401, 408, 414
420, 426, 431, 437, 443, 449, 455, 461, 467, 473, 479, 485, 491, 497, 503, 509, 515, 521, 527, 534, 540, 546, 552, 558
564, 570, 576, 582, 588, 594, 600, 606, 612, 618, 624, 630, 636, 642, 648, 654, 660, 666, 672, 678, 685, 691, 698, 703
709, 715, 721, 727, 733, 739, 745, 751, 757, 763, 769, 775, 781, 787, 793, 799, 805, 811, 817, 823, 829, 835, 841, 847
853, 859, 865, 871, 877, 883, 889, 895, 901, 907, 913, 919, 927, 932, 938, 944, 950, 956, 963, 969, 974, 981, 987, 993
999, 1004, 1010, 1016, 1022, 1028, 1034, 1040, 1046, 1052, 1058, 1064, 1104
    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.
FormatFile
Native Format (GENESIS format)    acc78.g   
MATLAB format    acc78.m   
SBML format    acc78.xml   
18 PKC
Pathway No. 364		 Ajay_Bhalla_
2007_Bistable
Accession No. 79		NetworkMolecule = 11
Enzyme   = 0
Reaction  = 10
Molecule = 0
Enzyme   = 0
Reaction  = 0
Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87/
2006-12-08 00:00:00
   Related Pathway: 
2, 20, 34, 55, 60, 71, 108, 123, 138, 147, 161, 181, 200, 207, 313, 330, 348, 370, 376, 383, 389, 395, 401, 408, 414
420, 426, 431, 437, 443, 449, 455, 461, 467, 473, 479, 485, 491, 497, 503, 509, 515, 521, 527, 534, 540, 546, 552, 558
564, 570, 576, 582, 588, 594, 600, 606, 612, 618, 624, 630, 636, 642, 648, 654, 660, 666, 672, 678, 685, 691, 698, 703
709, 715, 721, 727, 733, 739, 745, 751, 757, 763, 769, 775, 781, 787, 793, 799, 805, 811, 817, 823, 829, 835, 841, 847
853, 859, 865, 871, 877, 883, 889, 895, 901, 907, 913, 919, 927, 932, 938, 944, 950, 956, 963, 969, 974, 981, 987, 993
999, 1004, 1010, 1016, 1022, 1028, 1034, 1040, 1046, 1052, 1058, 1064, 1104
    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.
FormatFile
Native Format (GENESIS format)    acc79.g   
MATLAB format    acc79.m   
SBML format    acc79.xml   
19 PKC
Pathway No. 370		 Ajay_Bhalla_
2007_PKM
Accession No. 80		NetworkMolecule = 7
Enzyme   = 0
Reaction  = 5
Molecule = 0
Enzyme   = 0
Reaction  = 0
Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87/
2006-12-08 00:00:00
   Related Pathway: 
2, 20, 34, 55, 60, 71, 108, 123, 138, 147, 161, 181, 200, 207, 313, 330, 348, 364, 376, 383, 389, 395, 401, 408, 414
420, 426, 431, 437, 443, 449, 455, 461, 467, 473, 479, 485, 491, 497, 503, 509, 515, 521, 527, 534, 540, 546, 552, 558
564, 570, 576, 582, 588, 594, 600, 606, 612, 618, 624, 630, 636, 642, 648, 654, 660, 666, 672, 678, 685, 691, 698, 703
709, 715, 721, 727, 733, 739, 745, 751, 757, 763, 769, 775, 781, 787, 793, 799, 805, 811, 817, 823, 829, 835, 841, 847
853, 859, 865, 871, 877, 883, 889, 895, 901, 907, 913, 919, 927, 932, 938, 944, 950, 956, 963, 969, 974, 981, 987, 993
999, 1004, 1010, 1016, 1022, 1028, 1034, 1040, 1046, 1052, 1058, 1064, 1104
    This is a non-bistable model of ERKII signaling that also incorporates PKM synthesis triggered by Ca influx. It is a simplified variant of the model of Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80.
   
This pathway is part of accession 80 and is completely specified in the file acc80.g.
There is no separate files for just this pathway.
FormatFile
Native Format (GENESIS format)    acc80.g   
MATLAB format    acc80.m   
SBML format    acc80.xml   
20 PKC
Pathway No. 376		 Ajay_bhalla_
2007_ReacDiff1_
1e-12
Accession No. 81		NetworkMolecule = 7
Enzyme   = 0
Reaction  = 5
Molecule = 0
Enzyme   = 0
Reaction  = 0
Ajay_Bhalla_bistable_model. HFSP Journal. 2007 May;1(1):1-87/
2006-12-08 00:00:00
   Related Pathway: 
2, 20, 34, 55, 60, 71, 108, 123, 138, 147, 161, 181, 200, 207, 313, 330, 348, 364, 370, 383, 389, 395, 401, 408, 414
420, 426, 431, 437, 443, 449, 455, 461, 467, 473, 479, 485, 491, 497, 503, 509, 515, 521, 527, 534, 540, 546, 552, 558
564, 570, 576, 582, 588, 594, 600, 606, 612, 618, 624, 630, 636, 642, 648, 654, 660, 666, 672, 678, 685, 691, 698, 703
709, 715, 721, 727, 733, 739, 745, 751, 757, 763, 769, 775, 781, 787, 793, 799, 805, 811, 817, 823, 829, 835, 841, 847
853, 859, 865, 871, 877, 883, 889, 895, 901, 907, 913, 919, 927, 932, 938, 944, 950, 956, 963, 969, 974, 981, 987, 993
999, 1004, 1010, 1016, 1022, 1028, 1034, 1040, 1046, 1052, 1058, 1064, 1104
    This is a 25-compartment reaction-diffusion version of the Ajay_Bhalla_2007_PKM model. The original single-compartment model is repeated 25 times. In addition, a subset (27 out of 42) molecules can diffuse between compartments. Diffusion is implemented as a reaction between corresponding molecules in neighboring compartments. For D = 1e-12 m^2/sec (i.e., 1 micron^2/sec ) the kf and kb of this reaction for these 10 micron compartments are both 0.01/sec. For D = 1e-13 m^2/sec (i.e., 0.1 micron^2/sec ) the kf and kb are 0.001/sec.
The stimulus file pkm_mapk22_diff_1e-12_Fig4A which was used for the model to replicate Figure 4A from the paper.
This stimulus file pkm_mapk22_diff_1e-12_Fig4G which was used for the model to replicate Figure 4G from the paper
   
This pathway is part of accession 81 and is completely specified in the file acc81.g.
There is no separate file for just this pathway.
FormatFile
Native Format (GENESIS format)    acc81.g