affectors
Class Txn3aAff

java.lang.Object
  affectors.Affector
      affectors.Txn3aAff

All Implemented Interfaces:

java.lang.Cloneable

public class Txn3aAff

extends Affector

Txn3a takes two activators which synergize such that only in the presence of both can the target achieve full activity. Parameters include as usual the half-life of the target and the K's and nu's for each regulator, but also a "leak" parameter delta which enables one to specify that one of the two activators can reach some fraction (equal to delta) in the absence of the other (which behaves as a non-essential cofactor). Delta should range from 0 (no leak in the absence of cofactor) to at most 1.0 (cofactor has no effect). All inputs may be either cytoplasmic or membrane-bound as long as they reside in the same cell as the target.

Formula
ACTIVATION1 = ACTIVATOR1^nu_ACT1 / (K_ACT1^nu_ACT1 + ACTIVATOR1^nu_ACT1)
ACTIVATION2 = ACTIVATOR2^nu_ACT2 / (K_ACT2^nu_ACT2 + ACTIVATOR2^nu_ACT2)
dnodex/dt = (1 / H_nodex) * ACTIVATION1 * (delta + (1 - delta) * ACTIVATION2)

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
Leak fraction [delta_ACTIVATOR1nodex]	The fraction of activation achievable in the absence of the cofactor

Usage
&nodex

&Txn3aAff ACTIVATOR1 ACTIVATOR2 H_nodex K_ACTIVATOR1nodex nu_ACTIVATOR1nodex K_ACTIVATOR2nodex nu_ACTIVATOR2nodex delta_ACTIVATOR1nodex

&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

Txn3aAff()

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

Txn3aAff

public Txn3aAff()

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