affectors
Class Txn6aAff

java.lang.Object
  affectors.Affector
      affectors.Txn6aAff

All Implemented Interfaces:

java.lang.Cloneable

public class Txn6aAff

extends Affector

Txn6a takes two activators which synergize such that only in the presence of both can the target achieve full activity, and one inhibitor which reduces the effective concentration of the SECOND of these. This is like Txn3a but with an inhibitor that interferes with the cofactor. 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). All inputs may be either cytoplasmic or membrane-bound as long as they reside in the same cell as the target.

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

Parameters

Inhibitor [INHIBITOR]	The inhibitor Node
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
Half-max inhibition level [K_INHIBITOR]	The concentration of inhibitor at which half the cofactor is depleted
Inhibition Cooperativity [nu_INHIBITOR]	The non-linearity of the inhibiting function. The higher the value, the sharper the curves in the upside-down S-shaped inhibition function
Leak fraction [delta_ACTIVATOR1nodex]	The fraction of activation achievable in the absence of the cofactor

Usage
&nodex

&Txn6aAff INHIBITOR ACTIVATOR1 ACTIVATOR2 H_nodex K_ACTIVATOR1nodex nu_ACTIVATOR1nodex K_ACTIVATOR2nodex nu_ACTIVATOR2nodex K_INHIBITORnodex nu_INHIBITORnodex 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

Txn6aAff()

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

Txn6aAff

public Txn6aAff()

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