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) complexes
NFkB(loc~n,bin!0).IkBa(loc~n,pho~0,bin!0) # nuclear (NF-kB|IkB) complexes
NFkB(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 bin IkBa loc c pho 0 bin

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

NFkB loc n bin IkBa loc n pho 0 bin

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

NFkB loc c bin IkBa loc c pho p bin

Trash()

Trash

Observables

TNFR_a TNFR(st~a)

TNFR st a

TNFR_i TNFR(st~i)

TNFR st i

A20 A20()

A20

IKKK_a IKKK(st~a)

IKKK st a

IKK_a IKK(st~a)

IKK st a

NFkB_nuc NFkB(loc~n,bin)

NFkB loc n bin

NFkB_cyt NFkB(loc~c,bin)

NFkB loc c bin

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

NFkB loc c bin IkBa loc c pho p bin

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

NFkB loc c bin IkBa loc c pho 0 bin

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

NFkB loc n bin IkBa loc n pho 0 bin

TNF_ext TNF(loc~e)

TNF loc e

TNF_int TNF(loc~i)

TNF loc i

IKK_n IKK(st~n)

IKK st n

IKK_i IKK(st~i)

IKK st i

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

IkBa loc c pho p bin

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

IkBa loc c pho 0 bin

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

IkBa loc n pho 0 bin

tA20 A20_mRNA()

A20_mRNA

tIkB IkBa_mRNA()

IkBa_mRNA

tTNF TNF_mRNA()

TNF_mRNA

gA20_a GA20(st~1)

GA20 st 1

gA20_i GA20(st~0)

GA20 st 0

gTNF_a GTNF(st~1)

GTNF st 1

gTNF_i GTNF(st~0)

GTNF st 0

gIkBa_a GIkBa(st~1)

GIkBa st 1

gIkBa_i GIkBa(st~0)

GIkBa st 0

observables

IKK_tot_ IKK()

IKK st n a i ?ii

NFkB_tot_ NFkB()

NFkB loc n ?c ?bin

IKKK_tot_ IKKK()

IKKK st n ?a

Reaction Rules


TNFR1 activation and signal transduction cascade

TNF(loc~e) -> Trash()

TNF loc e degraded Trash synthesized

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⬆

GTNF(st~1) -> GTNF(st~1) + TNF_mRNA()

GTNF st 1 TNF_mRNA synthesized

GA20(st~1) -> GA20(st~1) + A20_mRNA()

GA20 st 1 A20_mRNA synthesized

GIkBa(st~1) -> GIkBa(st~1) + IkBa_mRNA()

GIkBa st 1 IkBa_mRNA synthesized

A20_mRNA() -> Trash()

A20_mRNA degraded Trash synthesized

IkBa_mRNA() -> Trash()

IkBa_mRNA degraded Trash synthesized

A20_mRNA() -> A20_mRNA() + A20()

A20_mRNA A20 synthesized

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

IkBa_mRNA IkBa loc c pho 0 bin synthesized

TNF_mRNA() -> Trash()

TNF_mRNA degraded Trash synthesized

TNF_mRNA() -> TNF_mRNA() + TNF(loc~i)

TNF_mRNA TNF loc i synthesized

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

A20() -> Trash()

A20 degraded Trash synthesized

IkBa(loc~c,pho~p,bin) -> Trash()

IkBa loc c pho p bin degraded Trash synthesized

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

NFkB loc c ⬆bin ⬆ IkBa loc c pho p ⬆bin degraded

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

IkBa loc c pho 0 bin degraded Trash synthesized

TNF(loc~i) -> Trash()

TNF loc i degraded Trash synthesized

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

NFkB loc c ⬆bin ⬆ IkBa loc c pho 0 ⬆bin degraded

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