Physiology

Reaction Diagram

reactionDiagram

Cross-References

Annotations

Reactions

Reactions
Name
Structure
Kinetics
EGFR EGF LR EGF_Binding_Unbinding compartment GeneralKinetics
LR EGFR_deg EGFReceptor_Degradation compartment GeneralKinetics
proEGFR EGFR EGFReceptor_Production compartment GeneralKinetics
EGFR EGFR_deg EGFReceptor_Degradation_Free compartment GeneralKinetics

EGF_Binding_Unbinding Universal ID's

EGF_Binding_Unbinding Text Annotations

EGFReceptor_Degradation Universal ID's

EGFReceptor_Degradation Text Annotations

EGFReceptor_Production Universal ID's

EGFReceptor_Production Text Annotations

EGFReceptor_Degradation_Free Universal ID's

EGFReceptor_Degradation_Free Text Annotations

Expressions for EGF_Binding_Unbinding

reaction rate

J

((k1_EGFR * EGF * EGFR) - (k2_EGFR * LR)) [mmol.ml-1.min-1]

Expressions for EGFReceptor_Degradation

reaction rate

J

(k1_deg * LR) [mmol.ml-1.min-1]

Expressions for EGFReceptor_Production

reaction rate

J

v_EGFR [mmol.ml-1.min-1]

Expressions for EGFReceptor_Degradation_Free

reaction rate

J

(k1_deg * EGFR) [mmol.ml-1.min-1]

Structures

Name
Type
Electrical
compartment Compartment (+)   (-)

compartment Universal ID's

compartment Text Annotations

Species

Name
Structure
BioNetGen Definition
Depiction
LR compartment EGFR(Y~U!1,State~active!-,).EGF(Site0!1,).
EGFR compartment EGFR(Y~U!-,State~active!-,).
EGFR_deg compartment EGFR(Y~U!-,State~deg!-,).
EGF compartment EGF(Site0!-,).
proEGFR compartment EGFR(Y~U!-,State~deg!-,).

LR Universal ID's

LR Text Annotations

EGFR Universal ID's

EGFR Text Annotations

EGFR_deg Universal ID's

EGFR_deg Text Annotations

EGF Universal ID's

EGF Text Annotations

proEGFR Universal ID's

proEGFR Text Annotations

Molecules

Name
BioNetGen Definition
DEPICTION
EGFR EGFR(Y~P~U,State~deg~active,)
EGF EGF(Site0,)
SOS SOS(Active~yes~no,)
Ras Ras(Active~yes~no,)
Raf Raf(Active~yes~no,)
MEK MEK(Active~yes~no,)
ERK ERK(Active~yes~no,)
P90Rsk P90Rsk(Active~yes~no,)
PI3K PI3K(Active~yes~no,)
Akt Akt(Active~yes~no,)
C3G C3G(Active~yes~no,)
Rap1 Rap1(Active~yes~no,)
B_Raf B_Raf(Active~yes~no,)
PP2A PP2A(Active~yes~no,)
P_tase P_tase()
GAP GAP()

EGFR Universal ID's

EGFR Text Annotations

EGF Universal ID's

EGF Text Annotations

SOS Universal ID's

SOS Text Annotations

Ras Universal ID's

Ras Text Annotations

Raf Universal ID's

Raf Text Annotations

MEK Universal ID's

MEK Text Annotations

ERK Universal ID's

ERK Text Annotations

P90Rsk Universal ID's

P90Rsk Text Annotations

PI3K Universal ID's

PI3K Text Annotations

Akt Universal ID's

Akt Text Annotations

C3G Universal ID's

C3G Text Annotations

Rap1 Universal ID's

Rap1 Text Annotations

B_Raf Universal ID's

B_Raf Text Annotations

PP2A Universal ID's

PP2A Text Annotations

P_tase Universal ID's

P_tase Text Annotations

GAP Universal ID's

GAP 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]
EGFR 80000.0 0.0 [m2/min]
EGFR_deg 0.0 0.0 [m2/min]
EGF 1.0002E7 0.0 [m2/min]
proEGFR 1.0 0.0 [m2/min]

Specifications (Reaction) - Deterministic go to Simulations

Name
Enabled?
EGF_Binding_Unbinding included
EGFReceptor_Degradation included
EGFReceptor_Production included
EGFReceptor_Degradation_Free included

Simulations - Deterministic go to Specifications

Name
End Time
Output Options
test 60.0

KeepEvery 1

KeepAtMost 1000

Deterministic Universal ID's

Deterministic Text Annotations

Global Parameters

Name
Expression
k1_deg 0.2[min-1]
v_EGFR 100.0[mmol.min-1.ml-1]
k1_EGFR 2.18503E-5[ml.min-1.mmol-1]
k2_EGFR 0.121008[min-1]

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