Statistical and Machine Learning Approaches for Network Analysis

1.2 Biological Networks

A network is a graph G(V, E) defined in terms of a set of vertices V and a set of edges E. In case of biological networks, a vertex is either a gene or protein encoded by an organism, and an edge e E joining two vertices in the network represents biological properties connecting and . A biological network can be directed or undirected depending on the biological relationship that used to join the pairs of vertices in the network. Both directed and undirected networks occur naturally in biological systems. Inference of these networks is a major challenge in systems biology. We briefly review two kinds of biological networks in the following sections.

1.2.1 Directed Networks

In directed networks, each edge is identified as an ordered pair of vertices. According to the Central Dogma of Molecular Biology, genetic information is encoded in double-stranded DNA. The information stored in DNA is transferred to single-stranded messenger RNA (mRNA) to direct protein synthesis [42]. Signal transduction is the primary mean to control the passage of biological information ...