Biology Reference
In-Depth Information
Fig. 2. HFPN model of interactions of genes
p53
,
MDM2
, and
p19ARF
and their products. For places and transitions, pictures
reflecting biological images are used (see Fig. 1). Biological meanings of transitions
T
1
,...,T
20
are summarized in Table 1.
understand the pathway. Each substance such as protein or mRNA corresponds to an HFPN element
“place” (originally a double circle, but it is changed to a picture reflecting the biological meaning of the
place: see Fig. 1 ), which holds the concentration of the substance. In Fig. 2 , each place is labeled with
the name of the substance (e.g. p53 mRNA, p19ARF). The name of a complex of two proteins A and
B is represented as A B, where places for proteins A and B are labeled with A and B. An additional
name (C) or (N) is attached at the tail of a substance name, when we need to distinguish locations of the
substances in the cytoplasm or in the nucleus.
Twenty-one biological events related to p53-MDM2 interactions are summarized in the second column
of Table 1, which have been extracted from the literature [Barak
et al.
, 1993; Miyashita and Reed, 1995;
Honda
et al.
, 1997; Kamijo
et al.
, 1998; Pomerantz
et al.
, 1998; Zhang
et al.
, 1998; Tao and Levine,
1999; Zhang and Xiong, 1999]. Each of these events is represented by an HFPN element “transition”
(originally an unfilled rectangle, but it is changed to a picture reflecting the biological meaning of the
