Interactomics

Interactomics is a discipline of bioinformatics and biology that deals with studying both the interactions and the consequences of those interactions between and among proteins, and other molecules within a cellcite journal | last =Kiemer | first=L | coauthors = G Cesareni | year = 2007| title = Comparative interactomics: comparing apples and pears? | journal= TRENDS in Biochemistry | volume = 25 |pages = 448–454 ] . These interactions are called the Interactome. Interactomics aims to compare networks of interaction between and within species to see how the traits of such networks are varied and conserved.

Interactomics is an example of "top-down" systems biology, which takes an overhead view of a system. Large sets of genome-wide data are collected, and correlations between different molecules are inferred. From the data new hypotheses are formulated about feedbacks between these molecules. These hypotheses can then be tested by new experimentscite journal | last =Bruggeman | first=F J | coauthors = H V Westerhoff| year = 2006| title = The nature of systems biology | journal= TRENDS in Microbiology | volume = 15 |pages = 45–50| doi = 10.1016/j.tim.2006.11.003] .

Through the study of the interaction of all of the molecules in a cell the field looks to gain a deeper understanding of genome function and evolution than just examining an individual genome in isolation. Interactomics goes beyond cellular proteomics in that it not only attempts to characterize the interaction between proteins, but between all molecules in the cell.

Methods of interactomics

The study of the interactome requires the collection of large amounts of data by way of high throughput experiments. Through these experiments a large number of data points are collected from a single organism under a small number of perturbations These experiments include:

*Two-hybrid screening
*Tandem Affinity Purification
*X-ray tomography
*Optical fluorescence microscopy

Recent developments

The field of interactomics is currently rapidly expanding and developing. While no biological interactomes have been fully characterized. Over 90% of proteins in "Saccharomyces cerevisiae" have been screened and their interactions characterized, making it the first interactome to be nearly fully specified [cite journal |last =Krogan |first= NJ | coauthors = et al. | year=2006|title = Global landscape of protein complexes in the yeast "Saccharomyeses Cerivisiae "| journal = Nature| volume= 440 |pages = 637–643|doi = 10.1038/nature04670] .

Also there have been recent systematic attempts to explore the human interactomeand [further citation needed] . Other species whose interactomes have been studied in some detail include "Caenorhabditis elegans" and "Drosophila melanogaster".

Criticisms and concerns

Kiemer and Cesareni raise the following concerns with the current state of the field:

*The experimental procedures associated with the field are error prone leading to "noisy results". This leads to 30% of all reported interactions being artifacts. In fact, two groups using the same techniques on the same organism found less than 30% interactions in common.
*Techniques may be biased, i.e. the technique determines which interactions are found.
*Ineractomes are not nearly complete with perhaps the exception of "S. cerivisiae".
*While genomes are stable, interactomes may vary between tissues and developmental stages.
*Genomics compares amino acids, and nucleotides which are in a sense unchangeable, but interactomics compares proteins and other molecules which are subject to mutation and evolution.
*It is difficult to match evolutionarily related proteins in distantly related species.

ee also

* Interaction network

References

External links

* [http://interactomics.org Interactomics.org] . A dedicated interactomics web site operated under BioLicense.
* [http://interactome.org Interactome.org] . An interactome wiki site.
* [http://psibase.kobic.re.kr PSIbase] Structural Interactome Map of all Proteins.
* [http://omics.org Omics.org] . An omics portal site that is openfree (under BioLicense)
* [http://genomics.org Genomics.org] . A Genomics wiki site.
* [http://bioinformatics.oxfordjournals.org/cgi/content/full/21/15/3234 Comparative Interactomics analysis of protein family interaction networks using PSIMAP (protein structural interactome map)]
* [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TYR-4KXVD30-2&_user=10&_coverDate=11%2F30%2F2006&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=8361bf3fe7834b4642cdda3b979de8bb Interaction interfaces in proteins via the Voronoi diagram of atoms]
* Using convex hulls to extract interaction interfaces from known structures. Panos Dafas, Dan Bolser, Jacek Gomoluch, Jong Park, and Michael Schroeder. Bioinformatics 2004 20: 1486-1490.
* PSIbase: a database of Protein Structural Interactome map (PSIMAP). Sungsam Gong, Giseok Yoon, Insoo Jang Bioinformatics 2005.
* Mapping Protein Family Interactions : Intramolecular and Intermolecular Protein Family Interaction Repertoires in the PDB and Yeast, Jong Park, Michael Lappe & Sarah A. Teichmann,J.M.B (2001).