Molecules

DNA_DSB()

DNA_DSB

ATM(S1981~0~P)

ATM S1981 0 P

SIAH1(S19~0~P)

SIAH1 S19 0 P

HIPK2()

HIPK2

Wip1()

Wip1

gene_Wip1(tf~0~1)

gene_Wip1 tf 0 1

mRNA_Wip1()

mRNA_Wip1

p53(S15_S20~0~PP,S46~0~P)

p53 S15_S20 0 PP S46 0 P

Mdm2(S166_S186~0~PP,S395~0~P,loc~Nuc~Cyt)

Mdm2 S166_S186 0 PP S395 0 P loc Nuc Cyt

gene_Mdm2(tf~0~1)

gene_Mdm2 tf 0 1

mRNA_Mdm2()

mRNA_Mdm2

PTEN()

PTEN

gene_PTEN(tf~0~1)

gene_PTEN tf 0 1

mRNA_PTEN()

mRNA_PTEN

PI3K()

PI3K

AKT(T308~0~P)

AKT T308 0 P

PtdIns(s~PP~PPP)

PtdIns s PP PPP

p21(b)

p21 b

mRNA_p21()

mRNA_p21

gene_p21(tf~0~1)

gene_p21 tf 0 1

Cyclin_E(b)

Cyclin_E b

Rb(S567~0~P,b)

Rb S567 0 P b

E2F1(b)

E2F1 b

Bax(b)

Bax b

gene_Bax(tf~0~1)

gene_Bax tf 0 1

mRNA_Bax()

mRNA_Bax

BclXL(b)

BclXL b

Bad(S75_S99~0~PP,b)

Bad S75_S99 0 PP b

Fourteen_3_3(b)

Fourteen_3_3 b

Caspase(csp~Pro~Act)

Caspase csp Pro Act

Species

SIAH1(S19~0)

SIAH1 S19 0

ATM(S1981~0)

ATM S1981 0

PI3K()

PI3K

PtdIns(s~PP)

PtdIns s PP

AKT(T308~0)

AKT T308 0

Rb(S567~0,b)

Rb S567 0 b

E2F1(b)

E2F1 b

BclXL(b)

BclXL b

Bad(S75_S99~0,b)

Bad S75_S99 0 b

Fourteen_3_3(b)

Fourteen_3_3 b

gene_Wip1(tf~0)

gene_Wip1 tf 0

gene_Mdm2(tf~0)

gene_Mdm2 tf 0

gene_p21(tf~0)

gene_p21 tf 0

gene_PTEN(tf~0)

gene_PTEN tf 0

gene_Bax(tf~0)

gene_Bax tf 0

Observables

DNA_DSB_tot DNA_DSB()

DNA_DSB

ATM_tot ATM()

ATM S1981 0 ?P

ATM_p ATM(S1981~P)

ATM S1981 P

gene_Wip1_on gene_Wip1(tf~1)

gene_Wip1 tf 1

mRNA_Wip1 mRNA_Wip1()

mRNA_Wip1

Wip1_tot Wip1()

Wip1

SIAH1_tot SIAH1()

SIAH1 S19 0 ?P

SIAH1_u SIAH1(S19~0)

SIAH1 S19 0

SIAH1_p SIAH1(S19~P)

SIAH1 S19 P

HIPK2_tot HIPK2()

HIPK2

p53_tot p53()

p53 S15_S20 0 ?PP S46 0 ?P

p53_0p p53(S15_S20~0,S46~0)

p53 S15_S20 0 S46 0

p53_arr p53(S15_S20~PP,S46~0)

p53 S15_S20 PP S46 0

p53_kill p53(S15_S20~PP,S46~P)

p53 S15_S20 PP S46 P

gene_Mdm2_on gene_Mdm2(tf~1)

gene_Mdm2 tf 1

mRNA_Mdm2 mRNA_Mdm2()

mRNA_Mdm2

Mdm2_tot Mdm2()

Mdm2 S166_S186 0 ?PP S395 0 ?P loc Nuc ?Cyt

Mdm2_cyt_0p Mdm2(S166_S186~0,S395~0,loc~Cyt)

Mdm2 S166_S186 0 S395 0 loc Cyt

Mdm2_cyt_2p Mdm2(S166_S186~PP,S395~0,loc~Cyt)

Mdm2 S166_S186 PP S395 0 loc Cyt

Mdm2_nuc_2p Mdm2(S166_S186~PP,S395~0,loc~Nuc)

Mdm2 S166_S186 PP S395 0 loc Nuc

Mdm2_nuc_3p Mdm2(S166_S186~PP,S395~P,loc~Nuc)

Mdm2 S166_S186 PP S395 P loc Nuc

PI3K_tot PI3K()

PI3K

gene_PTEN_on gene_PTEN(tf~1)

gene_PTEN tf 1

mRNA_PTEN mRNA_PTEN()

mRNA_PTEN

PTEN_tot PTEN()

PTEN

PIP2 PtdIns(s~PP)

PtdIns s PP

PIP3 PtdIns(s~PPP)

PtdIns s PPP

AKT_p AKT(T308~P)

AKT T308 P

gene_p21_on gene_p21(tf~1)

gene_p21 tf 1

mRNA_p21 mRNA_p21()

mRNA_p21

p21_tot p21()

p21 ?b

p21_free p21(b)

p21 b

CyclinE_tot Cyclin_E()

Cyclin_E ?b

CyclinE_free Cyclin_E(b)

Cyclin_E b

p21_CyclinE_cplx p21(b!4).Cyclin_E(b!4)

p21 b Cyclin_E b

Rb_tot Rb()

Rb S567 0 ?P ?b

Rb_p_free Rb(S567~P,b)

Rb S567 P b

E2F1_tot E2F1()

E2F1 ?b

E2F1_free E2F1(b)

E2F1 b

RB_u_E2F1_cplx Rb(S567~0,b!4).E2F1(b!4)

Rb S567 0 b E2F1 b

gene_Bax_on gene_Bax(tf~1)

gene_Bax tf 1

mRNA_Bax mRNA_Bax()

mRNA_Bax

Bax_tot Bax()

Bax ?b

Bax_free Bax(b)

Bax b

BclXL_tot BclXL()

BclXL ?b

BclXL_free BclXL(b)

BclXL b

Bax_BclXL_cplx Bax(b!1).BclXL(b!1)

Bax b BclXL b

Bad_tot Bad()

Bad S75_S99 0 ?PP ?b

Bad_free Bad(b)

Bad S75_S99 0 ?PP b

Bad_u_free Bad(S75_S99~0,b)

Bad S75_S99 0 b

Bad_p_free Bad(S75_S99~PP,b)

Bad S75_S99 PP b

BclXL_Bad_u_cplx BclXL(b!2).Bad(S75_S99~0,b!2)

BclXL b Bad S75_S99 0 b

Bad_p_14_3_3_cplx Bad(S75_S99~PP,b!3).Fourteen_3_3(b!3)

Bad S75_S99 PP b Fourteen_3_3 b

Fourteen_3_3_tot Fourteen_3_3()

Fourteen_3_3 ?b

Fourteen_3_3_free Fourteen_3_3(b)

Fourteen_3_3 b

Caspase_tot Caspase()

Caspase csp Pro ?Act

Caspase_pro Caspase(csp~Pro)

Caspase csp Pro

Caspase_act Caspase(csp~Act)

Caspase csp Act

Reaction Rules

gene_Wip1(tf~0) <-> gene_Wip1(tf~1)

gene_Wip1 tf 0 1 take all branches, once each, in any order⬇⬆

gene_Mdm2(tf~0) <-> gene_Mdm2(tf~1)

gene_Mdm2 tf 0 1 take all branches, once each, in any order⬇⬆

gene_p21(tf~0) <-> gene_p21(tf~1)

gene_p21 tf 0 1 take all branches, once each, in any order⬇⬆

gene_PTEN(tf~0) <-> gene_PTEN(tf~1)

gene_PTEN tf 0 1 take all branches, once each, in any order⬇⬆

gene_Bax(tf~0) <-> gene_Bax(tf~1)

gene_Bax tf 0 1 take all branches, once each, in any order⬇⬆

0 -> DNA_DSB()

DNA_DSB synthesized

0 -> DNA_DSB()

DNA_DSB synthesized

DNA_DSB() -> 0

DNA_DSB degraded

ATM(S1981~0) <-> ATM(S1981~P)

ATM S1981 0 P take all branches, once each, in any order⬇⬆

SIAH1(S19~0) <-> SIAH1(S19~P)

SIAH1 S19 0 P take all branches, once each, in any order⬇⬆

0 <-> HIPK2()

HIPK2 synthesized

0 <-> mRNA_Wip1()

mRNA_Wip1 synthesized

0 <-> mRNA_Wip1()

mRNA_Wip1 synthesized

0 <-> Wip1()

Wip1 synthesized

0 -> p53(S15_S20~0,S46~0)

p53 S15_S20 0 S46 0 synthesized

p53() -> 0

p53 S15_S20 0 ?PP S46 0 ?P degraded

p53(S15_S20~0,S46~0) -> 0

p53 S15_S20 0 S46 0 degraded

p53(S15_S20~0,S46~P) -> 0

p53 S15_S20 0 S46 P degraded

p53(S15_S20~PP,S46~0) -> 0

p53 S15_S20 PP S46 0 degraded

p53(S15_S20~PP,S46~P) -> 0

p53 S15_S20 PP S46 P degraded

p53(S15_S20~0) <-> p53(S15_S20~PP)

p53 S15_S20 0 PP take all branches, once each, in any order⬇⬆ S46 0 ?P

p53(S46~0) <-> p53(S46~P)

p53 S15_S20 0 ?PP S46 0 P take all branches, once each, in any order⬇⬆

0 <-> mRNA_Mdm2()

mRNA_Mdm2 synthesized

0 <-> mRNA_Mdm2()

mRNA_Mdm2 synthesized

0 -> Mdm2(S166_S186~0,S395~0,loc~Cyt)

Mdm2 S166_S186 0 S395 0 loc Cyt synthesized

Mdm2(S166_S186~0) -> 0

Mdm2 S166_S186 0 S395 0 ?P loc Nuc ?Cyt degraded

Mdm2(S166_S186~PP) -> 0

Mdm2 S166_S186 PP S395 0 ?P loc Nuc ?Cyt degraded

Mdm2(S166_S186~PP,S395~P,loc~Nuc) -> 0

Mdm2 S166_S186 PP S395 P loc Nuc degraded

Mdm2(S166_S186~0,S395~0,loc~Cyt) <-> Mdm2(S166_S186~PP,S395~0,loc~Cyt)

Mdm2 S166_S186 0 PP take all branches, once each, in any order⬇⬆ S395 0 loc Cyt

Mdm2(S166_S186~PP,S395~0,loc~Cyt) -> Mdm2(S166_S186~PP,S395~0,loc~Nuc)

Mdm2 S166_S186 PP S395 0 loc Nuc Cyt take one or more branches, once each, in any order⬆

Mdm2(S166_S186~PP,S395~0,loc~Nuc) <-> Mdm2(S166_S186~PP,S395~P,loc~Nuc)

Mdm2 S166_S186 PP S395 0 P take all branches, once each, in any order⬇⬆ loc Nuc

0 <-> mRNA_PTEN()

mRNA_PTEN synthesized

0 <-> mRNA_PTEN()

mRNA_PTEN synthesized

0 <-> PTEN()

PTEN synthesized

PtdIns(s~PP) <-> PtdIns(s~PPP)

PtdIns s PP PPP take all branches, once each, in any order⬇⬆

AKT(T308~0) <-> AKT(T308~P)

AKT T308 0 P take all branches, once each, in any order⬇⬆

0 <-> mRNA_p21()

mRNA_p21 synthesized

0 <-> mRNA_p21()

mRNA_p21 synthesized

0 <-> p21(b)

p21 b synthesized

0 <-> Cyclin_E(b)

Cyclin_E b synthesized

p21(b) + Cyclin_E(b) <-> p21(b!5).Cyclin_E(b!5)

p21 ⬇⬆b ⬇⬆ Cyclin_E ⬇⬆b

p21(b!5).Cyclin_E(b!5) -> 0

p21 ⬆b degraded ⬆ Cyclin_E ⬆b degraded

Rb(S567~0,b) <-> Rb(S567~P,b)

Rb S567 0 P take all branches, once each, in any order⬇⬆ b

Rb(S567~0,b) + E2F1(b) <-> Rb(S567~0,b!4).E2F1(b!4)

Rb S567 0 ⬇⬆b ⬇⬆ E2F1 ⬇⬆b

Rb(S567~0,b!4).E2F1(b!4) -> Rb(S567~P,b) + E2F1(b)

Rb S567 0 P take all branches, once each, in any order⬇ ⬆b ⬆ E2F1 ⬆b

0 <-> mRNA_Bax()

mRNA_Bax synthesized

0 <-> mRNA_Bax()

mRNA_Bax synthesized

0 <-> Bax(b)

Bax b synthesized

Bax(b) + BclXL(b) <-> Bax(b!1).BclXL(b!1)

Bax ⬇⬆b ⬇⬆ BclXL ⬇⬆b

Bax(b!1).BclXL(b!1) -> BclXL(b)

Bax ⬆b degraded ⬆ BclXL ⬆b

BclXL(b) + Bad(S75_S99~0,b) <-> BclXL(b!2).Bad(S75_S99~0,b!2)

BclXL ⬇⬆b ⬇⬆ Bad S75_S99 0 ⬇⬆b

BclXL(b!2).Bad(S75_S99~0,b!2) -> BclXL(b) + Bad(S75_S99~PP,b)

BclXL ⬆b ⬆ Bad S75_S99 0 PP take all branches, once each, in any order⬇ ⬆b

Bad(S75_S99~0,b) <-> Bad(b,S75_S99~PP)

Bad S75_S99 0 PP take all branches, once each, in any order⬇⬆ b

Bad(S75_S99~PP,b) + Fourteen_3_3(b) <-> Bad(b!3,S75_S99~PP).Fourteen_3_3(b!3)

Bad S75_S99 PP ⬇⬆b ⬇⬆ Fourteen_3_3 ⬇⬆b

Bad(S75_S99~PP,b!3).Fourteen_3_3(b!3) -> Bad(S75_S99~0,b) + Fourteen_3_3(b)

Bad S75_S99 0 PP take one or more branches, once each, in any order⬆ ⬆b ⬆ Fourteen_3_3 ⬆b

0 -> Caspase(csp~Pro)

Caspase csp Pro synthesized

Caspase() -> 0

Caspase csp Pro ?Act degraded

Caspase(csp~Pro) -> Caspase(csp~Act)

Caspase csp Pro Act take all branches, once each, in any order⬇