Protein Function Assignment through Mining Cross-Species Protein-Protein Interactions

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Issue Date
2008-02-06Author
Chen, Xue-wen
Liu, Mei
Ward, Robert E., IV
Publisher
Public Library of Science
Type
Article
Article Version
Scholarly/refereed, publisher version
Rights
©2008 Chen et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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BackgroundAs we move into the post genome-sequencing era, an immediate challenge is how to make best use of the large amount of high-throughput experimental data to assign functions to currently uncharacterized proteins. We here describe CSIDOP, a new method for protein function assignment based on shared interacting domain patterns extracted from cross-species protein-protein interaction data.Methodology/Principal FindingsThe proposed method is assessed both biologically and statistically over the genome of H. sapiens. The CSIDOP method is capable of making protein function prediction with accuracy of 95.42% using 2,972 gene ontology (GO) functional categories. In addition, we are able to assign novel functional annotations for 181 previously uncharacterized proteins in H. sapiens. Furthermore, we demonstrate that for proteins that are characterized by GO, the CSIDOP may predict extra functions. This is attractive as a protein normally executes a variety of functions in different processes and its current GO annotation may be incomplete.Conclusions/SignificanceIt can be shown through experimental results that the CSIDOP method is reliable and practical in use. The method will continue to improve as more high quality interaction data becomes available and is readily scalable to a genome-wide application.
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Citation
Chen, X., Liu, M., & Ward, R. (2008). Protein Function Assignment through Mining Cross-Species Protein-Protein Interactions. PLoS ONE, 3(2). http://dx.doi.org/10.1371/journal.pone.0001562
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Except where otherwise noted, this item's license is described as: ©2008 Chen et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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