Interactomics
Interactomics is a discipline at the intersection 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 cell.[1] The network of all such interactions is called the Interactome. Interactomics thus aims to compare such networks of interactions (i.e., interactomes) between and within species in order to find how the traits of such networks are either preserved or varied. From a mathematical, or mathematical biology viewpoint an interactome network is a graph or a category representing the most important interactions pertinent to the normal physiological functions of a cell or organism.
Interactomics is an example of "top-down" systems biology, which takes an overhead, as well as overall, view of a biosystem or organism. Large sets of genome-wide and proteomic 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 experiments.[2]
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.[1] Interactomics goes beyond cellular proteomics in that it not only attempts to characterize the interaction between proteins, but between all molecules in the cell.
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[edit] 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[2] These experiments include:
- Two-hybrid screening
- Tandem Affinity Purification
- X-ray tomography
- Optical fluorescence microscopy
[edit] 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.[3]
Also there have been recent systematic attempts to explore the human interactome[1] and.[additional citation needed]
Other species whose interactomes have been studied in some detail include Caenorhabditis elegans and Drosophila melanogaster.
[edit] Criticisms and concerns
Kiemer and Cesareni[1] 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.
[edit] See also
- Interaction network
- Proteomics
- Metabolic network
- Metabolic network modelling
- Metabolic pathway
- Genomics
- Mathematical biology
- Systems biology
[edit] References
- ^ a b c d Kiemer, L; G Cesareni (2007). "Comparative interactomics: comparing apples and pears?". TRENDS in Biochemistry 25 (10): 448–454. doi:10.1016/j.tibtech.2007.08.002. PMID 17825444.
- ^ a b Bruggeman, F J; H V Westerhoff (2006). "The nature of systems biology". TRENDS in Microbiology 15 (1): 45–50. doi:10.1016/j.tim.2006.11.003. PMID 17113776.
- ^ Krogan, NJ; et al. (2006). "Global landscape of protein complexes in the yeast Saccharomyeses Cerivisiae ". Nature 440 (7084): 637–643. doi:10.1038/nature04670. PMID 16554755.
[edit] External links
- Interactomics.org. A dedicated interactomics web site operated under BioLicense.
- Interactome.org. An interactome wiki site.
- PSIbase Structural Interactome Map of all Proteins.
- Omics.org. An omics portal site that is openfree (under BioLicense)
- Genomics.org. A Genomics wiki site.
- Comparative Interactomics analysis of protein family interaction networks using PSIMAP (protein structural interactome map)
- 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).
- Semantic Systems Biology
