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Pathway List for pkc

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
   Related Pathway: 
22034556071108123147161181200207313330348364370376383389395401408414
420426431437443449455461467473479485491497503509515521527534540546552558
564570576582588594600606612618624630636642648654660666672678685691698703
709715721727733739745751757763769775781787793799805811817823829835841847
853859865871877883889895901907913919927932938944950956963969974981987993
999100410101016102210281034104010461052105810641104
    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. 1104
 mTOR_pathway

Accession No. 92
NetworkMolecule = 11
Enzyme   = 0
Reaction  = 10
Molecule = 0
Enzyme   = 0
Reaction  = 0
Jain P, and Bhalla, U.S. PLoS Comput Biol. 2009 Feb;5(2). ( Peer-reviewed publication )/
2009-02-13
   Related Pathway: 
22034556071108123138147161181200207313330348364370376383389395401408
414420426431437443449455461467473479485491497503509515521527534540546552
558564570576582588594600606612618624630636642648654660666672678685691698
703709715721727733739745751757763769775781787793799805811817823829835841
847853859865871877883889895901907913919927932938944950956963969974981987
99399910041010101610221028103410401046105210581064
    This model consists of various sub-modules. They are as follows: 1) BDNF receptor signaling 2) AKT signaling 3) 4E-BP model 4) S6 Kinase model 5) CaMKIII model 6) Protein synthesis model 7) CaM 8) PKC 9) MAPK model.
   
This pathway is part of accession 92 and is completely specified in the file acc92.g.
There is no separate file for just this pathway.
FormatFile
Native Format (GENESIS format)    acc92.g   
3 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
   Related Pathway: 
234556071108123138147161181200207313330348364370376383389395401408414
420426431437443449455461467473479485491497503509515521527534540546552558
564570576582588594600606612618624630636642648654660666672678685691698703
709715721727733739745751757763769775781787793799805811817823829835841847
853859865871877883889895901907913919927932938944950956963969974981987993
999100410101016102210281034104010461052105810641104
    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   
4 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
   Related Pathway: 
22034556071108123138147161181200207313330348370376383389395401408414
420426431437443449455461467473479485491497503509515521527534540546552558
564570576582588594600606612618624630636642648654660666672678685691698703
709715721727733739745751757763769775781787793799805811817823829835841847
853859865871877883889895901907913919927932938944950956963969974981987993
999100410101016102210281034104010461052105810641104
    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   
5 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
   Related Pathway: 
22034556071108123138147161181200207313330348364376383389395401408414
420426431437443449455461467473479485491497503509515521527534540546552558
564570576582588594600606612618624630636642648654660666672678685691698703
709715721727733739745751757763769775781787793799805811817823829835841847
853859865871877883889895901907913919927932938944950956963969974981987993
999100410101016102210281034104010461052105810641104
    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   
6 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
   Related Pathway: 
22034556071108123138147161181200207313330348364370383389395401408414
420426431437443449455461467473479485491497503509515521527534540546552558
564570576582588594600606612618624630636642648654660666672678685691698703
709715721727733739745751757763769775781787793799805811817823829835841847
853859865871877883889895901907913919927932938944950956963969974981987993
999100410101016102210281034104010461052105810641104
    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   
7 PKC
Pathway No. 383
 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
   Related Pathway: 
22034556071108123138147161181200207313330348364370376389395401408414
420426431437443449455461467473479485491497503509515521527534540546552558
564570576582588594600606612618624630636642648654660666672678685691698703
709715721727733739745751757763769775781787793799805811817823829835841847
853859865871877883889895901907913919927932938944950956963969974981987993
999100410101016102210281034104010461052105810641104
    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   
8 PKC
Pathway No. 389
 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
   Related Pathway: 
22034556071108123138147161181200207313330348364370376383395401408414
420426431437443449455461467473479485491497503509515521527534540546552558
564570576582588594600606612618624630636642648654660666672678685691698703
709715721727733739745751757763769775781787793799805811817823829835841847
853859865871877883889895901907913919927932938944950956963969974981987993
999100410101016102210281034104010461052105810641104
    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   
9 PKC
Pathway No. 395
 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
   Related Pathway: 
22034556071108123138147161181200207313330348364370376383389401408414
420426431437443449455461467473479485491497503509515521527534540546552558
564570576582588594600606612618624630636642648654660666672678685691698703
709715721727733739745751757763769775781787793799805811817823829835841847
853859865871877883889895901907913919927932938944950956963969974981987993
999100410101016102210281034104010461052105810641104
    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   
10 PKC
Pathway No. 401
 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
   Related Pathway: 
22034556071108123138147161181200207313330348364370376383389395408414
420426431437443449455461467473479485491497503509515521527534540546552558
564570576582588594600606612618624630636642648654660666672678685691698703
709715721727733739745751757763769775781787793799805811817823829835841847
853859865871877883889895901907913919927932938944950956963969974981987993
999100410101016102210281034104010461052105810641104
    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   
11 PKC
Pathway No. 408
 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
   Related Pathway: 
22034556071108123138147161181200207313330348364370376383389395401414
420426431437443449455461467473479485491497503509515521527534540546552558
564570576582588594600606612618624630636642648654660666672678685691698703
709715721727733739745751757763769775781787793799805811817823829835841847
853859865871877883889895901907913919927932938944950956963969974981987993
999100410101016102210281034104010461052105810641104
    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   
12 PKC
Pathway No. 414
 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
   Related Pathway: 
22034556071108123138147161181200207313330348364370376383389395401408
420426431437443449455461467473479485491497503509515521527534540546552558
564570576582588594600606612618624630636642648654660666672678685691698703
709715721727733739745751757763769775781787793799805811817823829835841847
853859865871877883889895901907913919927932938944950956963969974981987993
999100410101016102210281034104010461052105810641104
    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   
13 PKC
Pathway No. 420
 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
   Related Pathway: 
22034556071108123138147161181200207313330348364370376383389395401408
414426431437443449455461467473479485491497503509515521527534540546552558
564570576582588594600606612618624630636642648654660666672678685691698703
709715721727733739745751757763769775781787793799805811817823829835841847
853859865871877883889895901907913919927932938944950956963969974981987993
999100410101016102210281034104010461052105810641104
    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   
14 PKC
Pathway No. 426
 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
   Related Pathway: 
22034556071108123138147161181200207313330348364370376383389395401408
414420431437443449455461467473479485491497503509515521527534540546552558
564570576582588594600606612618624630636642648654660666672678685691698703
709715721727733739745751757763769775781787793799805811817823829835841847
853859865871877883889895901907913919927932938944950956963969974981987993
999100410101016102210281034104010461052105810641104
    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   
15 PKC
Pathway No. 431
 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
   Related Pathway: 
22034556071108123138147161181200207313330348364370376383389395401408
414420426437443449455461467473479485491497503509515521527534540546552558
564570576582588594600606612618624630636642648654660666672678685691698703
709715721727733739745751757763769775781787793799805811817823829835841847
853859865871877883889895901907913919927932938944950956963969974981987993
999100410101016102210281034104010461052105810641104
    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   
16 PKC
Pathway No. 437
 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
   Related Pathway: 
22034556071108123138147161181200207313330348364370376383389395401408
414420426431443449455461467473479485491497503509515521527534540546552558
564570576582588594600606612618624630636642648654660666672678685691698703
709715721727733739745751757763769775781787793799805811817823829835841847
853859865871877883889895901907913919927932938944950956963969974981987993
999100410101016102210281034104010461052105810641104
    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   
17 PKC
Pathway No. 443
 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
   Related Pathway: 
22034556071108123138147161181200207313330348364370376383389395401408
414420426431437449455461467473479485491497503509515521527534540546552558
564570576582588594600606612618624630636642648654660666672678685691698703
709715721727733739745751757763769775781787793799805811817823829835841847
853859865871877883889895901907913919927932938944950956963969974981987993
999100410101016102210281034104010461052105810641104
    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   
18 PKC
Pathway No. 449
 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
   Related Pathway: 
22034556071108123138147161181200207313330348364370376383389395401408
414420426431437443455461467473479485491497503509515521527534540546552558
564570576582588594600606612618624630636642648654660666672678685691698703
709715721727733739745751757763769775781787793799805811817823829835841847
853859865871877883889895901907913919927932938944950956963969974981987993
999100410101016102210281034104010461052105810641104
    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   
19 PKC
Pathway No. 455
 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
   Related Pathway: 
22034556071108123138147161181200207313330348364370376383389395401408
414420426431437443449461467473479485491497503509515521527534540546552558
564570576582588594600606612618624630636642648654660666672678685691698703
709715721727733739745751757763769775781787793799805811817823829835841847
853859865871877883889895901907913919927932938944950956963969974981987993
999100410101016102210281034104010461052105810641104
    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   
20 PKC
Pathway No. 461
 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
   Related Pathway: 
22034556071108123138147161181200207313330348364370376383389395401408
414420426431437443449455467473479485491497503509515521527534540546552558
564570576582588594600606612618624630636642648654660666672678685691698703
709715721727733739745751757763769775781787793799805811817823829835841847
853859865871877883889895901907913919927932938944950956963969974981987993
999100410101016102210281034104010461052105810641104
    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   

 
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Database compilation and code copyright (C) 2005, Upinder S. Bhalla and NCBS/TIFR
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