Illustration of three types of network representations used in biological network analysis: Undirected network graph (e.g. used for protein–protein interaction network analysis); b) directed network graph (e.g. used for signaling network analysis of phosphorylation chains); c) directed network graph with activating interactions (e.g., from gene 1 to gene 2) and inhibiting interactions (e.g., from gene 3 and gene 4 to gene 1; used for transcriptional regulatory network analysis of activating and repressing transcription factor (TF)-target relationships). While regulatory and signaling network analyses take into account information about the topology, directionality, and nature of molecular interactions, most conventional pathway analyses do not fully incorporate this information.