Interactome

Interactome is the whole set of molecular interactions in cells. It is usually displayed as a directed graph. When spoken in terms of proteomics, it refers to protein-protein interaction network(PPI), or protein network (PN).

Methods of mapping the interactome
The study of the interactome is called interactomics. The basic unit of protein network is protein-protein interaction (PPI). Because the interactome considers the whole organism, there is a need to collect a massive amount of information.

Experimental methods have been devised to determine PPI, such as 1) affinity purification and 2) yeast two hybrid (Y2H). The former is suited to identify a protein complex, while the latter is suited to explore the binary interactions in mass quantities. The former is considered as a low-throughput method (LTP), while the latter is considered as high-throughput method (HTP).

There have been several efforts to map the eukaryotic interactome through HTP methods. Yeast, fly, worm, and human HTP maps have been created so far (2006).

Interactome databases

 * Database of interacting protein (DIP) (Xenarios et al. 2000)
 * GRID database
 * MIPS database
 * PSIMAP database: The first protein structural interactome DB
 * InterPare database: A structural protein interfaceome DB
 * Biomolecular Interaction Network Database (BIND) (Bader et al, 2003)
 * Online Predicted Human Interaction Database (OPHID) (Brown and Jurisica, 2005)
 * Human Protein Reference Database (HPRD) (Peri, S. et al, 2003)
 * Himap(Human Interactome Map)
 * HPID
 * MINT
 * PINdb
 * IntAct - The Molecular Interaction Database
 * APID - Agile Protein Interaction DataAnalyzer APID is interactive bioinformatic web-tool that integrates and unifies main known experimentally validated protein-protein interactions.