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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
Rb_dup participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1100010

Accession and Pathway Details
Accession NameAccession No.Accession TypePathway Link
  • Mammalian_cell_
    cycle
  • 85Network
    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
    NameAccession NamePathway NameInitial Conc.
    (uM)
    Volume
    (fL)
    Buffered
    Rb_dup
  • Mammalian_cell_
    cycle

    Accession No. : 85
  • Growth
    Pathway No. : 1069
    2200No

    Rb_dup acting as a Summed Molecule in  
    Mammalian_cell_cycle Network
    Accession NamePathway NameTargetInput
  • Mammalian_cell_
    cycle

    Accession No. : 85
  • Growth
    Pathway No. : 1069
    Rb_dupRb

    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.
    NameAccession NamePathway NameKfKbKdtauReagents
    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
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