Interactome

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

Contents 1 Methods of mapping the interactome 2 Interactome databases 3 See also 4 External links 5 References

[edit] 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).

[edit] Interactome databases

• Database of interacting protein (DIP) (Xenarios et al. 2000)
• GRID database
• MIPS database
• 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)
• HPID
• MINT
• PINdb
• IntAct - The Molecular Interaction Database

[edit] See also

• Bioinformatics
• List of omics topics in biology

[edit] External links

• Interactomics.org
• Interactome.org
• PSIbase Database. A global interactome DB

[edit] References

• 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.