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Studies offer guide as protein interaction mapping comes of age
Date:1/6/2009

interaction is indeed real, and not a false positive reading from a particular type of experiment. The kit is a set of four, high-capacity protein interaction tests that have been weighted in relation to a common set of benchmark data. When scientists identify two proteins as likely interactors, the pair can be tested in the tool kit to obtain a "confidence score" about whether they do, in fact, interact.

"This general approach will allow researchers to systematically and objectively assign confidence scores to all individual protein-protein interactions in cells," says lead author Pascal Braun, PhD. "Such a universally interpretable quality standard is critical for constructing accurate interactome maps."

The third study uses the quality control framework from the first study to compile a new, expanded map of the interactome of the worm Caenorhabditis elegans (C. elegans), a scientific favorite whose cells have roughly the same number of genes as human cells do. The previous version of the map was assembled from studies involving about 2,000 proteins. For the new map, lead author Nicolas Simonis, PhD, of the CCSB and his associates screened some 10,000 protein pairs, documenting 3,864 high quality interactions. The framework enabled the researchers to estimate that the worm's genome includes about 116,000 interactions, meaning that 96 percent of its interactome remains uncharted.

Trust, but verify

Interactome maps are constructed from a variety of sources -- new experiments and data from earlier studies. As Michael Cusick, PhD, and co-authors show in the fourth Nature Methods paper, the information in some of those much-used databases is not as reliable as one would hope.

The team focused on databases built from published studies that involve just a few protein interactions -- an approach sometimes thought to be more accurate than mass-screening techniques. Researchers typically cull information from severa
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Contact: Bill Schaller
william_schaller@dfci.harvard.edu
617-632-5357
Dana-Farber Cancer Institute
Source:Eurekalert

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