Biology Reference
In-Depth Information
Table 1
Biological facts extracted from the literature and assignments to transitions in the HFPN model of Fig. 2
Biological phenomena on the literature
#1
#2
Type of
Literature
biological
(obtained by experiments)
process
1
p53(N) is bound to MDM2(N), forming complex
p53 MDM2(N).
T
1
m
1*
m
2*0.01
binding
[Kamijo
et al.
, 1998,
Zhang
et al.
, 1998]
2
MDM2(N) is bound to p19ARF(N), forming com-
plex MDM2 p19ARF.
T
2
m
2*
m
4*0.01
binding
[Kamijo
et al.
, 1998,
Pomerantz
et al.
, 1998,
Zhang
et al.
, 1998]
3
p53 MDM2(N) is bound to p19ARF(N), forming
complex p53 MDM2(N) p19ARF.
T
3
m
4*
m
5*0.01
binding
[Kamijo
et al.
, 1998,
Zhang
et al.
, 1998]
4
MDM2 p19ARF is bound to p53(N), forming
complex p53 MDM2(N) p19ARF.
T
4
m
1*
m
6*0.01
binding
[Kamijo
et al.
, 1998,
Zhang
et al.
, 1998]
5
Transcription of injected gene
p53
, producing p53
mRNA.
T
5
1
transcription
−
T
6
6
p53 mRNA is translated to p53(C).
m
10*0.1
translation
[Kamijo
et al.
, 1998,
Pomerantz
et al.
, 1998]
T
7
m
5*0.1
7
p53 MDM(N) is exported from the nucleus to the
cytoplasm (p53
MDM(C)).
nuclear export
[Tao and Levine, 1999,
Zhang and Xiong, 1999]
8
p53
is
marked
with
ubiquitin
(multiubiquitin
T
8
m
7*
m
8*0.01
ubiquitination
[Honda
et al.
, 1997]
chain) (p53[Ub]).
9
Polyubiquitinated p53 (p53[Ub]) is destroyed by
proteasome.
T
9
m
9*0.5
degradation
[Honda
et al.
, 1997,
Pomerantz
et al.
, 1998]
10
Protein MDM2 (MDM2(C)) is imported from the
cytoplasm to the nucleus (MDM2(N)).
T
10
m
12*0.1
nuclear import
[Tao and Levine, 1999,
Zhang and Xiong, 1999]
11
Protein p53 (p53(C)) is imported from the cyto-
plasm to the nucleus (p53(N)).
T
11
m
11*0.1
nuclear import
[Tao and Levine, 1999,
Zhang and Xiong, 1999]
12
Transcription of injected gene
MDM2
, producing
MDM2 mRNA.
T
12
1
transcription
[Kamijo
et al.
, 1998,
Pomerantz
et al.
, 1998]
13
MDM2 mRNA is translated to MDM2(C).
T
13
m
13*0.1
translation
[Kamijo
et al.
, 1998,
Pomerantz
et al.
, 1998]
14
Transcription of injected gene
p19ARF
, produc-
T
14
1
transcription
[Kamijo
et al.
, 1998,
Pomerantz
et al.
, 1998]
ing p19ARF mRNA.
15
p19ARF mRNA is translated to
p19ARF(C).
T
15
m
15*0.1
translation
[Kamijo
et al.
, 1998,
Pomerantz
et al.
, 1998]
16
Protein p19ARF (p19ARF(C)) is imported from
the cytoplasm to the nucleus (p19ARF(N)).
T
16
m
16*0.1
nuclear import
[Tao and Levine, 1999]
17
Protein p53 (p53(N)) activates transcription of
gene
Bax
, producing Bax mRNA.
T
17
m
1*0.1
transcription
[Miyashita and Reed, 1995]
18
Protein
p53
(p53(N))
activates
transcription
T
18
m
1*0.1
transcription
[Barak
et al.
,1993]
of
gene
MDM2
,
producing
MDM2
mRNA.
(endogenous).
19
Stabilizing p53 complex (p53 MDM2 p19ARF)
activates transcription of gene
Bax
, producing
Bax mRNA.
T
19
m
3*0.1
transcription
−
T
20
m
3*0.1
−
20
Stabilizing p53 complex (p53 MDM2 p19ARF)
activates transcription of gene
MDM2
, producing
MDM2 mRNA.
transcription
21
p19ARF could not affect to p53 transactivation
without Protein MDM2.
−
transcription
[Kamijo
et al.
, 1998]
(#1: Corresponding transitions in the HFPN, #2: Speed of corresponding transitions in the HFPN.
mX
(
X
=1
,...,
20
)isthe
concentration of a corresponding substance in Table 2.)
transition: see Fig. 1), where the reaction speed of the event is assigned. Twenty biological events are
assigned to the transitions
T
i
(
i
=
1,
...
,20) as shown in the third column of Table 1. Types of biological
