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).
- 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)
- 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.
- PSIbase Database. A global interactome DB based on PSIMAP
- Interactome.org. A dedicated interactome web site.
- Bader GD, et al. (2003) BIND: The Biomolecular interaction Network Database. Nucleic Acids Res., 31, 248-50.
- Brown KR, Jurisica I. (2005) Online Predicted Human Interaction Database. Bioinformatics, 21(9): 2076-82.
- Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM, Eisenberg D. (2000) DIP: the database of interacting proteins. Nucleic Acids Res. 28: 289-91.
- Peri S., Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK, et al. (2003) Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res 13:2363-71.
- Park J, Lappe M, Teichmann SA. (2001) Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. J Mol Biol. 2001 Mar 30;307(3):929-38.
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