| |
Pathway Name
Pathway No. | Accession Name
Accession No. | Accession
Type | Pathway statistics | CaRegulation statistics | Source
Entry Date |
| 1 | CaRegulation
Pathway No. 86 | Synaptic_
Network
Accession No. 16 | Network | Molecule = 11
Enzyme = 1
Reaction = 4
| 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 |
| | #6Related Pathway:
11, 110, 132, 149, 170 |
| | This simple implementation of Ca regulation includes three compartments: the extracellular, the intracellular, and the Ca stores. Pumps maintain the Ca levels in cytoplasm (pumping out to the extracellular space and into the stores). Leak channels from the stores and extracellular space balance it out. Finally, the IP3 receptor and the capacitive entry channel respond to stimuli of various kinds. One clear direction for further work is to incorporate various calcium buffering proteins such as calsequestrin into the model. Primary reference is from the book Receptors: Models for binding, trafficking and signaling, by Lauffenburger and Linderman, OUP, 1993, Ch 5, around pg 200. There is extensive reference to a submitted paper by Mahama and Linderman, whose published version appears to be Mahama and Linderman 1994 Biophys J 67(3):1345-1357 This model is a little artificial on the IP3R kinetics and does not include the Ca influence on IP3R. |
| | 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 |
|
| 2 | CaRegulation
Pathway No. 132 | Osc_Ca_
IP3metabolism
Accession No. 24 | Network | Molecule = 16
Enzyme = 1
Reaction = 9
| 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 |
| | #6Related Pathway:
11, 86, 110, 149, 170 |
| | Modified Ca Regulation model for the IP3 metabolism network. This model is used with the Othmer-Tang model for IP3 receptor kinetics, to generate cytosolic Ca oscillations. Channel kinetics of the IP3 receptor, ER-leak, ER-pump (or CaATPase) and Capacitative Ca entry have been modified to allow for Ca oscillations characterized in the Othmer-Tang model (Tang et al, Biophys J 70, 1996: 246-63). Kinetics of store Ca buffering by Calsequestrin have not been changed. |
| | 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 |
|
| 3 | CaRegulation
Pathway No. 170 | Osc_Ca_
IP3metabolism
Accession No. 32 | Network | Molecule = 16
Enzyme = 1
Reaction = 9
| 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 |
| | #6Related Pathway:
11, 86, 110, 132, 149 |
| | Modified Ca Regulation model for the IP3 metabolism network. This model is used with the Othmer-Tang model for IP3 receptor kinetics, to generate cytosolic Ca oscillations. Channel kinetics of the IP3 receptor, ER-leak, ER-pump (or CaATPase) and Capacitative Ca entry have been modified to allow for Ca oscillations characterized in the Othmer-Tang model (Tang et al, Biophys J 70, 1996: 246-63). Kinetics of store Ca buffering by Calsequestrin have not been changed. |
| | 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 |
|
| 4 | CaRegulation
Pathway No. 110 | NonOsc_Ca_
IP3metabolism
Accession No. 23 | Network | Molecule = 22
Enzyme = 1
Reaction = 12
| 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 |
| | #6Related Pathway:
11, 86, 132, 149, 170 |
| | Ca Regulation model used for the IP3metabolism network. It includes 3 compartments: extracellular, intracellular and the Ca stores. Ca pumps that pump out Ca from cytoplasm to extracellular space and into stores, are balanced by leak channels from the stores and extracellular space. The IP3 receptor and capacitative entry channels drive Ca under influence of different stimuli. Model includes the Ca buffer - Calsequestrin in the stores. The model is a little artificial on IP3R kinetics, and does not include the influence of Ca on IP3R. |
| | 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 | CaRegulation
Pathway No. 149 | NonOsc_Ca_
IP3metabolism
Accession No. 31 | Network | Molecule = 22
Enzyme = 1
Reaction = 12
| 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 |
| | #6Related Pathway:
11, 86, 110, 132, 170 |
| | Ca Regulation model used for the IP3metabolism network. It includes 3 compartments: extracellular, intracellular and the Ca stores. Ca pumps that pump out Ca from cytoplasm to extracellular space and into stores, are balanced by leak channels from the stores and extracellular space. The IP3 receptor and capacitative entry channels drive Ca under influence of different stimuli. Model includes the Ca buffer - Calsequestrin in the stores. The model is a little artificial on IP3R kinetics, and does not include the influence of Ca on IP3R. |
| | 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 |
|
| 6 | CaRegulation
Pathway No. 11 | fig2_egfr
Accession No. 1 | Network | Molecule = 11
Enzyme = 1
Reaction = 4
| 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 |
| | #6Related Pathway:
86, 110, 132, 149, 170 |
| | 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. |
| Format | File | | Native Format (GENESIS format) | acc1.g | | GENESIS Format (Annotated version) | Anno_acc1.g |
|
or Pathway 