Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
PI3K PI3K_act PI3K_Activation_EGFR cell GeneralKinetics
PI3K PI3K_act PI3K_Activation_Ras cell GeneralKinetics
PI3K_act PI3K PI3K_Deactivation cell GeneralKinetics

PI3K_Activation_EGFR Universal ID's

PI3K_Activation_EGFR Text Annotations

PI3K_Activation_Ras Universal ID's

PI3K_Activation_Ras Text Annotations

PI3K_Deactivation Universal ID's

PI3K_Deactivation Text Annotations

Expressions for PI3K_Activation_EGFR

reaction rate

J

(Kcat_act * LR * PI3K / (km_act + PI3K)) [mmol.ml-1.min-1]

Expressions for PI3K_Activation_Ras

reaction rate

J

(Kcat_PI3Kact * Ras_act * PI3K / (km_PI3K_act + PI3K)) [mmol.ml-1.min-1]

Expressions for PI3K_Deactivation

reaction rate

J

(k1_act * PI3K_act) [mmol.ml-1.min-1]

Structures

Name
Type
Electrical
cell Compartment (+)   (-)

cell Universal ID's

cell Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
LR cell EGF(EGF!1,).EGFR(ecd!1,Y~P!-,).
Ras_act cell Ras(Active~yes!-,).
PI3K_act cell PI3K(Active~yes!-,).
PI3K cell PI3K(Active~no!-,).

LR Universal ID's

LR Text Annotations

Ras_act Universal ID's

Ras_act Text Annotations

PI3K_act Universal ID's

PI3K_act Text Annotations

PI3K Universal ID's

PI3K Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION
EGFR EGFR(ecd,Y~P~U,)
EGF EGF(EGF,)
Ras Ras(Active~yes~no,)
PI3K PI3K(Active~yes~no,)

EGFR Universal ID's

EGFR Text Annotations

EGF Universal ID's

EGF Text Annotations

Ras Universal ID's

Ras Text Annotations

PI3K Universal ID's

PI3K Text Annotations

Observables

Name
Structure
Count
BNGL Definition
Sequence Type
DEPICTION

Applications

Name
Properties Math Type
Deterministic Specs - Species
Specs - Reaction
Simulations 		Deterministic (ODE) Compartmental

Deterministic Text Annotations

Deterministic Universal ID's

Annotations will come here

RFID | pubmed

Specifications (Species) - Deterministic go to Simulations

Species
Initial Condition
Diffusion Constant
LR 0.0 0.0 [m2/min]
Ras_act 0.0 0.0 [m2/min]
PI3K_act 0.0 0.0 [m2/min]
PI3K 120000.0 0.0 [m2/min]

Specifications (Reaction) - Deterministic go to Simulations

Name
Enabled?
PI3K_Activation_EGFR included
PI3K_Activation_Ras included
PI3K_Deactivation included

Simulations - Deterministic go to Specifications

Name
End Time
Output Options

Global Parameters

Name
Expression
Kcat_act 10.6737[min-1]
km_act 184912.0[mmol.ml-1]
km_PI3K_act 272056.0[mmol.ml-1]
Kcat_PI3Kact 0.0771067[min-1]
k1_act 0.005[min-1]

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Universal ID's

Text Annotations

Downloads

Format
File
VCML VCML File
BNGL
MatLab
SBML
Formatted XML
SEDML