Boolean network-based analysis of the apoptosis network (Mai and Liu 2009)

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Accession:144586
"To understand the design principles of the molecular interaction network associated with the irreversibility of cell apoptosis and the stability of cell surviving, we constructed a Boolean network integrating both the intrinsic and extrinsic pro-apoptotic pathways with pro-survival signal transduction pathways. We performed statistical analyses of the dependences of cell fate on initial states and on input signals. The analyses reproduced the well-known pro- and anti-apoptotic effects of key external signals and network components. We found that the external GF signal by itself did not change the apoptotic ratio from randomly chosen initial states when there is no external TNF signal, but can significantly offset apoptosis induced by the TNF signal. ..."
Reference:
1 . Mai Z, Liu H (2009) Boolean network-based analysis of the apoptosis network: irreversible apoptosis and stable surviving J Theor Biol 259(4):760-9 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Molecular Network;
Brain Region(s)/Organism: Generic;
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON; Python;
Model Concept(s): Methods; Signaling pathways; Boolean network; Apoptosis;
Implementer(s): Neymotin, Sam [samn at neurosim.downstate.edu];
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anetdemo
readme.html
bnet.mod
misc.mod *
stats.mod *
vecst.mod *
apopnames.txt
apoprules.txt
bnet.py
dbgnames.txt
dbgrules.txt
declist.hoc *
decmat.hoc *
decnqs.hoc *
decvec.hoc *
default.hoc *
grvec.hoc *
init.hoc
local.hoc *
misc.h *
misc.py *
mosinit.py
netstate.gif
network.py
nqs.hoc *
nrnoc.hoc *
pyinit.py *
python.hoc
pywrap.hoc *
simctrl.hoc *
snutils.py
                            
TNF:ON:1 -> TNFR1
TNF:OFF:-1 -> TNFR1

TNFR1:ON:1  -> TRADD
TNFR1:OFF:-1 -> TRADD

TRADD:ON:1 -> TRAF
TRADD:OFF:-1 -> TRAF

TRADD:ON:1 -> FADD
TRADD:OFF:-1 -> FADD

TRADD:ON:1 -> RIP
TRADD:OFF:-1 -> RIP

TRAF:ON:1 -> cFLIP
TRAF:OFF:-1 -> cFLIP

FADD:ON:1 -> Cas8
Cas6:ON:1 -> Cas8
cFLIP:ON:-1 -> Cas8
FADD,Cas6:OFF,OFF:-1 -> Cas8

TNF:ON:1 -> TNFR2
TNF:OFF:-1 -> TNFR2

RIP:ON:1 -> TRAF2
TNFR2:ON:-2 -> TRAF2
RIP:OFF:-1 -> TRAF2

TRAF2:ON:1 -> NIK
TRAF2:OFF:-1 -> NIK

NIK:ON:1 -> IKK
Akt:ON:1 -> IKK
A20:ON:-3 -> IKK
// next old
// NIK,Akt:OFF,OFF:-1 -> IKK
// next new
IKK:ON:-1 -> IKK

NFkB:ON:1 -> IkB
IKK:ON:-2 -> IkB

IkB:OFF:1 -> NFkB
IkB:ON:-1 -> NFkB

NFkB:ON:1 -> A20
NFkB:OFF:-1 -> A20

TRAF:ON:1 -> MEKK1
TRAF:OFF:-1 -> MEKK1

MEKK1:ON:1 -> JNKK
MEKK1:OFF:-1 -> JNKK
Akt:ON:-2 -> JNKK

JNKK:ON:1 -> JNK
JNKK:OFF:-1 -> JNK

Cas8:ON:1 -> Cas7
APC:ON:1 -> Cas7
IAP:ON:-3 -> Cas7
// next old
// Cas8,APC:OFF,OFF:-1 -> Cas7
// next new
Cas7:ON:-1 -> Cas7

Cas7:ON:1 -> Cas12
Cas7:OFF:-1 -> Cas12

Cas12:ON:1 -> Cas9
Cas3:ON:1 -> Cas9
Akt:ON:-1 -> Cas9
// next 1 old
// Cas12:OFF:-1 -> Cas9
// next 1 new
Cas12,Cas3:OFF,OFF:-1 -> Cas9
// next 1 old
// IAP:ON:-2 -> Cas9
// next 1 new
IAP:ON:-3 -> Cas9

Cas9,Apaf1,Mito:ON,ON,ON:1 -> APC
IAP:ON:-2 -> APC
// next 3 old
// Cas9:OFF:-1 -> APC
// Apaf1:OFF:-1 -> APC
// Mito:OFF:-1 -> APC
// next new
APC:ON:-1 -> APC

Cas8:ON:1 -> Cas3
APC:ON:1 -> Cas3
Cas6:ON:1 -> Cas3
// next 1 old
// IAP:ON:-4 -> Cas3
// next 1 new (weight of -5 vs -4)
IAP:ON:-5 -> Cas3
// next 1 old
// Cas8,APC,Cas6:OFF,OFF,OFF:-1 -> Cas3
// next 1 new
Cas3:ON:-1 -> Cas3

Cas3:ON:1 -> Cas6
IAP:ON:-2 -> Cas6
Cas3:OFF:-1 -> Cas6

p53,JNK:ON,ON:1 -> BID
p53,Cas8:ON,ON:1 -> BID
BcIX:ON:-3 -> BID
p53:OFF:-1 -> BID

NFkB:ON:1 -> BcIX
p53:ON:-1 -> BcIX
BAD:ON:-2 -> BcIX
NFkB:OFF:-1 -> BcIX

p53:ON:1 -> BAD
Akt:ON:-2 -> BAD
p53:OFF:-1 -> BAD

JNK:ON:1 -> p53
DNADamage:ON:3 -> p53
Mdm2:ON:-2 -> p53
// next 1 old
// JNK,DNADamage:OFF,OFF:-1 -> p53
// next 1 new
p53:ON:-1 -> p53

p53:ON:1 -> Apaf1
p53:OFF:-1 -> Apaf1

p53:ON:1 -> PTEN
p53:OFF:-1 -> PTEN

BID:ON:1 -> Mito
BcIX:ON:-1 -> Mito

NFkB:ON:1 -> IAP
Mito:ON:-1 -> IAP
Cas3,Cas6:ON,ON:-1 -> IAP

GF:ON:1 -> GFR
GF:OFF:-1 -> GFR

GFR:ON:1 -> PI3K
GFR:OFF:-1 -> PI3K

GFR:ON:1 -> PIP2
GFR:OFF:-1 -> PIP2

PI3K,PIP2:ON,ON:1 -> PIP3
PIP2:OFF:-1 -> PIP3
PTEN:ON:-2 -> PIP3

PIP3:ON:1 -> Akt
PIP3:OFF:-1 -> Akt

Akt:ON:1 -> Mdm2
p53:ON:1 -> Mdm2
// next 1 old
// Akt:OFF:-1 -> Mdm2
// next 1 new
Mdm2:ON:-1 -> Mdm2

Cas3:ON:1 -> DNADamage
// DNADamage:ON:-1 -> DNADamage

DNADamage:ON:1 -> Apoptosis

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