Protein Network

A protein network is a representation of relationships among proteins, commonly their physical interactions with one another. In a protein-protein interaction (PPI) network, each protein is represented as a node and each represented interaction as a link, or edge, connecting two nodes. Such networks provide a systems-level view of how proteins are organized through interactions rather than examining each protein in isolation .^1,2

Protein networks can range from small networks centered on a particular biological process to large interaction maps containing thousands of proteins. The collection of protein-protein interactions considered for a cell or organism is often referred to as its protein interactome. Interactions used to construct these maps can be identified experimentally, including through binary interaction assays and methods that isolate protein complexes, or inferred using computational approaches .¹

A connection in a protein network does not necessarily mean that two proteins are permanently bound. Protein interactions can be stable or transient, and which interactions occur can depend on factors such as cell type, location, physiological state, and experimental conditions. Interaction maps are also incomplete and influenced by the methods used to detect interactions, so they are best understood as representations of available interaction data rather than complete maps of every interaction occurring simultaneously in a cell .^1,2

A protein network is distinct from a protein complex. A protein complex is a physical assembly of associated proteins, whereas a network is an abstract representation that can connect many proteins and complexes through multiple interactions .¹