affectors
Class Txn4DipAff

java.lang.Object
  affectors.Affector
      affectors.Txn4DipAff

All Implemented Interfaces:

java.lang.Cloneable

public class Txn4DipAff

extends Affector

Diploid version of Txn4Aff. Reduces to same result if the two alleles are identical. Assumptions for diploidizing: Txn4 takes two activators and one inhibitor which titrates away the *second* activator. Parameters include not just the half-life of the target and the K's and nu's for each regulator, but also the weights alpha and beta, which determine the relative effectiveness of each activator. All inputs may be either cytoplasmic or membrane-bound as long as they reside in the same cell as the target.

Formula
INHIBITION_LEVEL = ( 1 - (INHIBITOR^nu_INHIB / (K_INHIBITOR^nu_INHIB + INHIBITOR^nu_INHIB)) )
ACTIVATION1 = ACTIVATOR1^nu_ACT1 / (K_ACT1^nu_ACT1 + ACTIVATOR1^nu_ACT1)
ACTIVATION2 = (ACTIVATOR2 * INHIBITION_LEVEL)^nu_ACT2 / (K_ACT2^nu_ACT2 + (ACTIVATOR2 * INHIBITION_LEVEL)^nu_ACT2)
dnodex/dt = (1 / H_nodex) * (alpha * ACTIVATION1) + (beta * ACTIVATION2) / (1 + (alpha * ACTIVATION1) + (beta * ACTIVATION2))

Parameters

Inhibitor [INHIBITOR]	The inhibitor Node
Activator1 [ACTIVATOR1]	The first transcriptional activator Node
Activator2 [ACTIVATOR2]	The second transcriptional activator Node, the target of the inhibitor
mRNA Half-life [H_nodex]	The half life of the product mRNA
Half-max activation level for first activator [K_ACTIVATOR1nodex]	The concentration of the first activator at which transcription proceeds at half its maximal rate
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
Saturability coefficient for Activator 1 [alpha_nodex]	determines how completely the first activator can saturate the promoter
Half-max activation level for second activator [K_ACTIVATOR2nodex]	The concentration of the second activator at which transcription proceeds at half its maximal rate
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
Saturability coefficient for Activator 2 [beta_nodex]	determines how completely the second activator can saturate the promoter
Half-max inhibition level [K_INHIBITOR]	The concentration of inhibitor at which transcription proceeds at half the rate it would have otherwise
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

Usage
&nodex

&Txn4Aff INHIBITOR ACTIVATOR1 ACTIVATOR2 H_nodex K_ACTIVATOR1nodex nu_ACTIVATOR1nodex alpha K_ACTIVATOR2nodex nu_ACTIVATOR2nodex beta K_INHIBITORnodex nu_INHIBITORnodex

&endnodex

NOTE - you can accomplish this same function using the meta-enhancers, and those are a more general framework for putting together transcription terms.

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

Txn4DipAff()

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

Txn4DipAff

public Txn4DipAff()

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