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Molecule Parameter List for Rb_dup | The statistics table lists the distribution of a molecule acting either as a substrate, product, enzyme or as a molecule within the network.
The text color of a molecule is highlighted by  color. | | Statistics |
Accession and Pathway Details | |
| Accession Name | Accession No. | Accession Type | Pathway Link | Mammalian_cell_
cycle | 85 | Network |
Growth, CELLDIV, Rb_grp,
IE_GRP, CycB_Grp, Cdc20_Grp,
Cdh1_grp, E2F, CycA_Grp,
CycE_grp, Early_Response_Genes, Delayed_Response_Genes,
CycD_Grp | | This is a fairly complete mass-action reimplementation of the Novak and Tyson mammalian cell cycle model. It is inexact on two counts. First, it replaces many rather abstracted equations with mass action and Michaelis-Menten forms of enzymes. Second, it does not handle the halving of cellular volume at the division point. Within these limitations, the model does most of what the original paper shows including oscillation of the relevant molecules. |
Rb_dup acting as a Molecule in Mammalian_cell_cycle Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | Rb_dup | Mammalian_cell_
cycle
Accession No. : 85 | Growth
Pathway No. : 1069 | 2 | 200 | No |
Rb_dup acting as a Summed Molecule in Mammalian_cell_cycle Network
Rb_dup acting as a Substrate in a reaction in Mammalian_cell_cycle Network
| Kd is calculated only for second order reactions, like nA+nB <->nC or nA<->nC+nD, where n is number and A,B,C,D are molecules, where as for first order reactions Keq is calculated.
Kd for higher order reaction are not consider. |
| Name | Accession Name | Pathway Name | Kf | Kb | Kd | tau | Reagents | | H1 | Mammalian_cell_
cycle
Accession No. : 85 | Growth
Pathway No. : 1069 | 0.2
(uM^-4 s^-1) | 125
(s^-1) | - | - | Substrate
Heaviside_inh
Rb_dup
Rb_dup
Rb_dup
Rb_dup
Product
Heaviside_mid
| | This reaction approximates the Heaviside function. What it does is to present a high-order dependence on Rb_P, such that when Rb_P is about 0.8 of the total It is supposed to be 1 if Rb_hypo <= 0.8 Rb_tot. Here we have Rb_P = Rb_tot - Rb_hypo, so we want the outcome to be 1 if Rb_P > 0.2 We use a 4th order step to get a sharper transition. Use a sumtotal so that Rb_P itself is not affected. 29 March 2005. Now this is part of a 2-step heaviside function, perhaps more biologically motivated. Also the input is Rb. 18 Apr 2005. Speeded up 10 fold. Also note that the critical amount of Rb is Rb/Rbtot. Since Rbtot = 10, the Kd should be 8, not 0.8. |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
This Copyright is applied to ensure that the contents of this database remain freely available. Please see FAQ for details. |
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