affectors
Class TxnSiteActInhibit2Aff

java.lang.Object
  affectors.Affector
      affectors.TxnSiteActInhibit2Aff

All Implemented Interfaces:

java.lang.Cloneable

public class TxnSiteActInhibit2Aff

extends Affector

Use for activation + inhibition of transcription. Activates according to an S-shaped function (Phi function) with a half maximal activation level K and a cooperativity nu. Inhibits by multiplying the activator concentration by an upside down-S shaped inhibition function (Psi function). This is identical to the Txn2aAff except that it is designed to work inside of a meta-affector, and models the situation in which the inhibitor reduces the effective concentration of the activator, rather than reducing the effectiveness of bound activator (see TxnSiteActInhibitAff for this option) or throttling the activator's effect by multiplying Phi by Psi (see TxnSiteActInhibit3Aff for this option). This family is designed to work inside of a meta-affector. You should only use this Affector inside of an EnhancerRegion.

Formula
inhibit_term = 1 - [(INHIBITOR/K_inhibit)^nu_inhibit * / (1 + (INHIBITOR/K_inhibit)^nu_inhibit)]
dnodex/dt = ((ACTIVATOR * inhibit_term)/K_act)^nu / (1 + ((ACTIVATOR * inhibit_term)/K)^nu)

Parameters

Activator [ACTIVATOR]	The transcriptional activator Node
Inhibitor [INHIBITOR]	The transcriptional inhibitor Node
Half-max activation level of activator [K_ACTIVATORnodex]	The concentration of activator at which transcription proceeds at half the maximal rate this particular "site" is capable of driving, absent inhibition
Cooperativity of activator [nu_ACTIVATORnodex]	The non-linearity of the activating function. The higher the value, the sharper the curves in the S-shaped activation function
Half-max inhibition level of inhibitor [K_INHIBITORnodex]	The concentration of inhibitor at which the activator's effective concentration is reduced by half
Cooperativity of inhibitor [nu_INHIBITORnodex]	The non-linearity of the inhibition function. The higher the value, the sharper the curves in the S-shaped inhibition function

Usage
&nodex

&EnhancerRegion H_nodex

&TxnSiteActivatorAff ACTIVATOR INHIBITOR K_ACTIVATORnodex nu_ACTIVATORnodex K_INHIBITORnodex nu_INHIBITORnodex

&endEnhancerRegion

&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

TxnSiteActInhibit2Aff()

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

TxnSiteActInhibit2Aff

public TxnSiteActInhibit2Aff()

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