affectors
Class Txn3bAff

java.lang.Object
  affectors.Affector
      affectors.Txn3bAff

All Implemented Interfaces:

java.lang.Cloneable

public class Txn3bAff

extends Affector

Txn3b takes two activators which synergize such that the second makes the first more potent. Parameters include as usual the half-life of the target and the K's and nu's for each regulator, but also a parameter eta which determines how much the potentiator changes the half-maximal activation level (K_ACT1) for the primary activator. Eta should range between 1 (no potentiation) to 10 (10-fold potentiation). NOTE: pay attention to the formula; the second activator in effect lowers K_ACT1, which may already be a small number. Half-maximal coefficients should not be allowed to become unrealistically small or one would run the risk of parameters such that fractional numbers of molecules would effect transcriptional activation! Therefore this affector limits the effect of the potentiator to a ten-fold reduction in K_ACT1. All inputs may be either cytoplasmic or membrane-bound as long as they reside in the same cell as the target.

Formula
ACTIVATION2 = ACTIVATOR2^nu_ACT2 / (K_ACT2^nu_ACT2 + ACTIVATOR2^nu_ACT2)
effective_K_ACT1 = K_ACT1 * (1 - (1 - (1 / Max[10,eta])) * ACTIVATION2)
dnodex/dt = (1 / H_nodex) * ACTIVATOR1^nu_ACT1 / (effective_K_ACT1^nu_ACT1 + ACTIVATOR1^nu_ACT1)

Parameters

Activator1 [ACTIVATOR1]	The first transcriptional activator Node
Activator2 [ACTIVATOR2]	The second transcriptional activator Node, the "cofactor"
mRNA Half-life [H_nodex]	The half life of the product mRNA
Half-max activation level for first activator [K_ACTIVATOR1nodex]	The half-maximal concentration of the first activator
Activator 1 cooperativity [nu_ACTIVATOR1nodex]	The non-linearity for the first activator. The higher the value, the sharper the curves in the S-shaped activation function
Half-max activation level for second activator [K_ACTIVATOR2nodex]	The half-maximal concentration of the cofactor
Activator 2 cooperativity [nu_ACTIVATOR2nodex]	The non-linearity for the second activator. The higher the value, the sharper the curves in the S-shaped activation function
Potentiation [eta_ACTIVATOR1nodex]	The factor by which the potentiator reduces the hald-maximal concentration of the primary activator

Usage
&nodex

&Txn3bAff ACTIVATOR1 ACTIVATOR2 H_nodex K_ACTIVATOR1nodex nu_ACTIVATOR1nodex K_ACTIVATOR2nodex nu_ACTIVATOR2nodex eta_ACTIVATOR2nodex

&endnodex

Field Summary

Fields inherited from class affectors.Affector

ADesc, affectorType, CC, CERTIFICATION, CONVERSION, copyNumber, DEGRADATION, FF, firstFreeParam, GG, GUI_CAPABLE, HH, KK, MATHTYPE, NDesc, PDesc, PRODUCTION, RETURNS_DERIV, RETURNS_PARTIALS, TERMTYPE, TT, Type, UNSPECIFIED

Constructor Summary

Txn3bAff()

Method Summary

float	getValue(Node which_node)
protected void	setLabelsAndTypes()
void	setParameterNumbers(int[] param_nums)

Methods inherited from class affectors.Affector

addDefaultParam, Chi, clearStatic, copy_, copy, doesContainTarget, findOrCreateParam, findParam, fixNodes, getNCValue, getNodes, getNumNodes, getNumParameters, getOtherSide, getParameter, getParameter, getParamName, getParamPos, getParamValue, getParamValue, getParamVariationMode, init, isLinearInTarget, Phi, Psi, setContainsTarget, setDescriptions, setParameter, setParamRange, setParamRange, setParamValue, setParamValue, setSide, setSided

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Txn3bAff

public Txn3bAff()

Method Detail

setLabelsAndTypes

protected void setLabelsAndTypes()

Specified by:

setLabelsAndTypes in class Affector

setParameterNumbers

public void setParameterNumbers(int[] param_nums)

Specified by:

setParameterNumbers in class Affector

getValue

public float getValue(Node which_node)

Overrides:

getValue in class Affector