affectors
Class Txn2aDipAff

java.lang.Object
  affectors.Affector
      affectors.Txn2aDipAff

All Implemented Interfaces:

java.lang.Cloneable

public class Txn2aDipAff

extends Affector

Diploid version of Txn2bAff. Reduces to same result if the two alleles are identical. Assumptions for diploidizing:

Txn2a implements transcriptional activation under the control of one activator and one inhibitor, the latter of which competetively inhibits the activator. The inhibitor behaves as if it titrates away the activator according to some dose-response curve; another way to look at it is that the inhibitor raises the threshhold for activation. The activator and inhibitor may be either cytoplasmic or membrane-bound, as long as both are in the same cell as the target.

Formula
EFFECTIVE_ACT = ACTIVATOR(neighbors) * ( 1 - INHIBITOR^nu_INHIB / (K_INHIBITOR^nu_INHIB + INHIBITOR^nu_INHIB))
dnodex/dt = (1 / H_nodex) * EFFECTIVE_ACT^nu_ACT / (K_ACT^nu_ACT + EFFECTIVE_ACT^nu_ACT)

Parameters

Inhibitor 1 [INHIBITOR1]	The inhibitor allele 1 Node
Inhibitor 2 [INHIBITOR2]	The inhibitor allele 2 Node
Activator 1 [ACTIVATOR1]	The transcriptional activator allele 1 Node
Activator 2 [ACTIVATOR2]	The transcriptional activator allele 2 Node
Half-max activation level allele 1 [K_ACTIVATOR1nodex]	The concentration of activator allele 1 at which transcription proceeds at half its maximal rate
Half-max activation level allele 2 [K_ACTIVATOR2nodex]	The concentration of activator allele 2 at which transcription proceeds at half its maximal rate
Activator Cooperativity allele 1 [nu_ACTIVATOR1nodex]	The non-linearity of the activating function allele 1. The higher the value, the sharper the curves in the S-shaped activation function
Activator Cooperativity allele 2 [nu_ACTIVATOR2nodex]	The non-linearity of the activating function allele 2. The higher the value, the sharper the curves in the S-shaped activation function
mRNA Half-life [H_nodex]	The half life of the product mRNA
Half-max inhibition level allele 1 on activator allele 1 [K_INHIBITOR11]	The concentration of inhibitor allele 1 on activator allele 1 at which transcription proceeds at half the rate it would have otherwise
Half-max inhibition level allele 1 on activator allele 2 [K_INHIBITOR12]	The concentration of inhibitor allele 1 on activator allele 2 at which transcription proceeds at half the rate it would have otherwise
Half-max inhibition level allele 2 on activator allele 1 [K_INHIBITOR21]	The concentration of inhibitor allele 2 on activator allele 1 at which transcription proceeds at half the rate it would have otherwise
Half-max inhibition level allele 2 on activator allele 2 [K_INHIBITOR22]	The concentration of inhibitor allele 2 on activator allele 2 at which transcription proceeds at half the rate it would have otherwise
Inhibition Cooperativity allele 1 on activator allele 1 [nu_INHIBITOR11]	The non-linearity of the inhibiting function allele 1 on activator allele 1. The higher the value, the sharper the curves in the upside-down S-shaped inhibition function
Inhibition Cooperativity allele 1 on activator allele 2 [nu_INHIBITOR12]	The non-linearity of the inhibiting function allele 1 on activator allele 2. The higher the value, the sharper the curves in the upside-down S-shaped inhibition function
Inhibition Cooperativity allele 2 on activator allele 1 [nu_INHIBITOR21]	The non-linearity of the inhibiting function allele 2 on activator allele 1. The higher the value, the sharper the curves in the upside-down S-shaped inhibition function
Inhibition Cooperativity allele 2 on activator allele 2 [nu_INHIBITOR22]	The non-linearity of the inhibiting function allele 2 on activator allele 2. The higher the value, the sharper the curves in the upside-down S-shaped inhibition function

Usage
&nodex

&Txn2aDipAff INHIBITOR1 INHIBITOR2 ACTIVATOR1 ACTIVATOR2 K_ACTIVATOR1nodex K_ACTIVATOR2nodex nu_ACTIVATOR1nodex nu_ACTIVATOR1nodex H_nodex K_INHIBITOR1nodex K_INHIBITOR2nodex nu_INHIBITOR1nodex nu_INHIBITOR2nodex

&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

Txn2aDipAff()

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

Txn2aDipAff

public Txn2aDipAff()

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