Interactome

Interactome is defined as the whole set of molecular interactions in cells. It is usually displayed as a directed graph. Molecular interactions can occur between molecules belonging to different biochemical families (proteins, nucleic acids, lipids, carbohydrates, ....) and also within a given family. When spoken in terms of proteomics, interactome refers to protein-protein interaction network(PPI), or protein interaction network (PIN). Another extensively studied type of interactome is the protein-DNA interactome (network formed by transcription factors (and DNA or chromatin regulatory proteins) and their target genes. The word "interactome" was originally coined in 1999 by a group of french scientists headed by Bernard Jacq (see Nucleic acids research 27(1):89-94; PubMed ID: 9847149). There are now nearly 300 research articles indexed with the word "interactome" (http://www.ncbi.nlm.nih.gov/sites/entrez) and more than 140 000 Google pages (http://www.google.fr/search?hl=fr&q=interactome&btnG=Recherche+Google&meta=).

It has been suggested that the size of an organism's interactome correlates better than genome size with the biological complexity of the organism (Stumpf, et al., 2008). Although protein-protein interaction maps containing several thousands of binary interactions are now available for several organisms, none of them is presently complete and the size of interactomes is still a matter of debate.

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

• APID - Agile Protein Interaction DataAnalyzer APID is interactive bioinformatic web-tool that integrates and unifies main known experimentally validated protein-protein interactions (Prieto and De Las Rivas, 2006).
• Database of interacting proteins (DIP) (Xenarios et al. 2000).
• BioGRID 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 Proteins Interacting in the Nucleus Database (Luc PV and Tempst P, 2004)
• IntAct - The Molecular Interaction Database
• VirHostNet - Virus-Host protein-protein interaction Networks knowledgebase

See also

• Bioinformatics
• Omics
• List of omics topics in biology

External links

• PSIbase Database. A global interactome DB based on PSIMAP
• Interactome.org A dedicated interactome web site.

References

• Sanchez C, Lachaize C, Janody F, Bellon B, Röder L, Euzenat J, Rechenmann F, Jacq B. (1999) Grasping at molecular interactions and genetic networks in Drosophila melanogaster using FlyNets, an Internet database. Nucleic Acids Res. 27(1):89-94.
• 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.
• Stumpf M, Thorne T, et al. (2008) Estimating the size of the human interactome Proceedings of the National Academy of Sciences, 105(19): 6959