Pathway, Functional Units
Pathway refers to a functional path in the biological networks. Generally, it corresponds to a signal, energy, or metabolite flow. In metabolic networks, it is often called metabolic pathways as a whole. In protein-protein interaction networks, it is often the same as the signaling pathways. In gene regulatory networks, it often means the mechanism under which expression quantitative trait loci regulate the expression of their target transcripts. In KEGG (Hiroyuki Ogata et al. 1999), the pathway concept is also extended to cell communication, organismal systems, diseases, and drug responses.
Pathway is characterized basically by its connectivity, orientation, functionality, and dynamics. These four characteristics apply to all types of pathways, including metabolic pathways, signaling pathways, and gene regulatory pathways.
In metabolic networks, a metabolic pathway means a set of chemical reactions occurring within a cell in which a principal chemical is...