Mathematical modeling of the molecular switch of TNFR1-mediated signaling pathways applying Petri net formalism and in silico knockout analysis
Fig 2
The PN model of TNFR1 signal transduction.
The PN consists of 118 places drawn as white or gray circles, 130 transitions drawn as black squares, and 299 directed edges. Logical places were colored gray, describing vertices with equal names that represent one vertex in the underlying data structure of the PN. The essential processes of NF-κB activation, apoptosis, and necroptosis were shaded blue, green, and red, respectively. The initial marking was represented by one token (black dot) assigned to the places IκB_g, A20_g, XIAP_g, cFLIP_g, and BCL-2_g (g stands for gene) for each place invariant (PI).