Molecules

TNFR(st~a~i)

TNFR st a i

IKK(st~n~a~i~ii)

IKK st n a i ii

IKKK(st~n~a)

IKKK st n a

IkBa(loc~n~c,pho~0~p,bin)

IkBa loc n c pho 0 p bin

IkBa_mRNA()

IkBa_mRNA

A20()

A20

A20_mRNA()

A20_mRNA

NFkB(loc~n~c,bin)

NFkB loc n c bin

TNF(loc~e~i)

TNF loc e i

TNF_mRNA()

TNF_mRNA

GIkBa(st~0~1)

GIkBa st 0 1

GA20(st~0~1)

GA20 st 0 1

GTNF(st~0~1)

GTNF st 0 1

Trash()

Trash
NFkB(loc~c,bin!0).IkBa(loc~c,pho~0,bin!0) # cytoplasmic (NF-kB|IkB) complexesNFkB(loc~n,bin!0).IkBa(loc~n,pho~0,bin!0) # nuclear (NF-kB|IkB) complexesNFkB(loc~c,bin!0).IkBa(loc~c,pho~p,bin!0) # phosphorylated cytoplasmic IkB complexed to NF-kB

Species

TNFR(st~a)

TNFR st a

TNFR(st~i)

TNFR st i

IKK(st~n)

IKK st n

IKK(st~a)

IKK st a

IKK(st~i)

IKK st i

IKK(st~ii)

IKK st ii

IKKK(st~n)

IKKK st n

IKKK(st~a)

IKKK st a

IkBa(loc~n,pho~p,bin)

IkBa loc n pho p bin

IkBa(loc~n,pho~0,bin)

IkBa loc n pho 0 bin

IkBa(loc~c,pho~0,bin)

IkBa loc c pho 0 bin

IkBa_mRNA()

IkBa_mRNA

A20()

A20

A20_mRNA()

A20_mRNA

NFkB(loc~n,bin)

NFkB loc n bin

NFkB(loc~c,bin)

NFkB loc c bin

TNF(loc~e)

TNF loc e

TNF(loc~i)

TNF loc i

TNF_mRNA()

TNF_mRNA

GIkBa(st~0)

GIkBa st 0

GIkBa(st~1)

GIkBa st 1

GA20(st~0)

GA20 st 0

GA20(st~1)

GA20 st 1

GTNF(st~0)

GTNF st 0

GTNF(st~1)

GTNF st 1

NFkB(loc~c,bin!0).IkBa(loc~c,pho~0,bin!0)

NFkB loc c 0bin IkBa loc c pho 0 0bin

NFkB(loc~n,bin!0).IkBa(loc~n,pho~0,bin!0)

NFkB loc n 0bin IkBa loc n pho 0 0bin

NFkB(loc~c,bin!0).IkBa(loc~c,pho~p,bin!0)

NFkB loc c 0bin IkBa loc c pho p 0bin

Trash()

Trash

Observables

TNFR(st~a)

TNFR st a

TNFR(st~i)

TNFR st i

A20()

A20

IKKK(st~a)

IKKK st a

IKK(st~a)

IKK st a

NFkB(loc~n,bin)

NFkB loc n bin

NFkB(loc~c,bin)

NFkB loc c bin

NFkB(loc~c,bin!0).IkBa(loc~c,pho~p,bin!0)

NFkB loc c 0bin IkBa loc c pho p 0bin

NFkB(loc~c,bin!0).IkBa(loc~c,pho~0,bin!0)

NFkB loc c 0bin IkBa loc c pho 0 0bin

NFkB(loc~n,bin!0).IkBa(loc~n,pho~0,bin!0)

NFkB loc n 0bin IkBa loc n pho 0 0bin

TNF(loc~e)

TNF loc e

TNF(loc~i)

TNF loc i

IKK(st~n)

IKK st n

IKK(st~i)

IKK st i

IkBa(loc~c,pho~p,bin)

IkBa loc c pho p bin

IkBa(loc~c,pho~0,bin)

IkBa loc c pho 0 bin

IkBa(loc~n,pho~0,bin)

IkBa loc n pho 0 bin

A20_mRNA()

A20_mRNA

IkBa_mRNA()

IkBa_mRNA

TNF_mRNA()

TNF_mRNA

GA20(st~1)

GA20 st 1

GA20(st~0)

GA20 st 0

GTNF(st~1)

GTNF st 1

GTNF(st~0)

GTNF st 0

GIkBa(st~1)

GIkBa st 1

GIkBa(st~0)

GIkBa st 0
observables

IKK()

IKK st n a i ii

NFkB()

NFkB loc n c bin

IKKK()

IKKK st n a

Reaction Rules

TNFR1 activation and signal transduction cascade

TNFR(st~i) + TNF(loc~e) -> TNFR(st~a) + TNF(loc~e)

TNFR st a i take one or more branches, once each, in any order⬆⬆ TNF loc e

TNFR(st~i) + TNF(loc~i) -> TNFR(st~a) + TNF(loc~i)

TNFR st a i take one or more branches, once each, in any order⬆⬆ TNF loc i

TNFR(st~a) -> TNFR(st~i)

TNFR st a i take all branches, once each, in any order⬇⬇

IKKK(st~n) -> IKKK(st~a)

IKKK st n a take all branches, once each, in any order⬇⬇

IKKK(st~a) -> IKKK(st~n)

IKKK st n a take one or more branches, once each, in any order⬆⬆

IKK(st~n) -> IKK(st~a)

IKK st n a take all branches, once each, in any order⬇⬇

IKK(st~a) -> IKK(st~i)

IKK st a i take all branches, once each, in any order⬇⬇

IKK(st~i) -> IKK(st~ii)

IKK st i ii take all branches, once each, in any order⬇⬇

IKK(st~ii) -> IKK(st~n)

IKK st n ii take one or more branches, once each, in any order⬆⬆
IkB, A20 and TNF gene expression

NFkB(loc~n,bin) + GA20(st~0) -> NFkB(loc~n,bin) + GA20(st~1)

NFkB loc n bin GA20 st 0 1 take all branches, once each, in any order⬇⬇

NFkB(loc~n,bin) + GIkBa(st~0) -> NFkB(loc~n,bin) + GIkBa(st~1)

NFkB loc n bin GIkBa st 0 1 take all branches, once each, in any order⬇⬇

IkBa(loc~n,pho~0,bin) + GA20(st~1) -> IkBa(loc~n,pho~0,bin) + GA20(st~0)

IkBa loc n pho 0 bin GA20 st 0 1 take one or more branches, once each, in any order⬆⬆

IkBa(loc~n,pho~0,bin) + GIkBa(st~1) -> IkBa(loc~n,pho~0,bin) + GIkBa(st~0)

IkBa loc n pho 0 bin GIkBa st 0 1 take one or more branches, once each, in any order⬆⬆

NFkB(loc~n,bin) + GTNF(st~0) -> NFkB(loc~n,bin) + GTNF(st~1)

NFkB loc n bin GTNF st 0 1 take all branches, once each, in any order⬇⬇

IkBa(loc~n,pho~0,bin) + GTNF(st~1) -> IkBa(loc~n,pho~0,bin) + GTNF(st~0)

IkBa loc n pho 0 bin GTNF st 0 1 take one or more branches, once each, in any order⬆⬆

GTNF(st~1) -> GTNF(st~0)

GTNF st 0 1 take one or more branches, once each, in any order⬆⬆
Protein interactions

NFkB(loc~c,bin) + IkBa(loc~c,pho~0,bin) -> NFkB(loc~c,bin!0).IkBa(loc~c,pho~0,bin!0)

NFkB loc c 0 ⬇bin IkBa loc c pho 0 0 ⬇bin

NFkB(loc~n,bin) + IkBa(loc~n,pho~0,bin) -> NFkB(loc~n,bin!0).IkBa(loc~n,pho~0,bin!0)

NFkB loc n 0 ⬇bin IkBa loc n pho 0 0 ⬇bin

IkBa(loc~c,pho~0,bin) + IKK(st~a) -> IkBa(loc~c,pho~p,bin) + IKK(st~a)

IkBa loc c pho 0 p take all branches, once each, in any order⬇⬇ bin IKK st a

NFkB(loc~c,bin!0).IkBa(loc~c,pho~0,bin!0) + IKK(st~a) -> NFkB(loc~c,bin!0).IkBa(loc~c,pho~p,bin!0) + IKK(st~a)

NFkB loc c 0bin IkBa loc c pho 0 p take all branches, once each, in any order⬇⬇ 0bin IKK st a
Transport

NFkB(loc~c,bin) -> NFkB(loc~n,bin)

NFkB loc n c take one or more branches, once each, in any order⬆⬆ bin

IkBa(loc~c,pho~0,bin) -> IkBa(loc~n,pho~0,bin)

IkBa loc n c take one or more branches, once each, in any order⬆⬆ pho 0 bin

IkBa(loc~n,pho~0,bin) -> IkBa(loc~c,pho~0,bin)

IkBa loc n c take all branches, once each, in any order⬇⬇ pho 0 bin

NFkB(loc~n,bin!0).IkBa(loc~n,pho~0,bin!0) -> NFkB(loc~c,bin!0).IkBa(loc~c,pho~0,bin!0)

NFkB loc n c take all branches, once each, in any order⬇⬇ 0bin IkBa loc n c take all branches, once each, in any order⬇⬇ pho 0 0bin