Faster and more accurate global protein function assignment from protein interaction networks using the MFGO algorithm

FEBS Letters
Shiwei SunDongbo Bu

Abstract

Predicting protein function accurately is an important issue in the post-genomic era. To achieve this goal, several approaches have been proposed deduce the function of unclassified proteins through sequence similarity, co-expression profiles, and other information. Among these methods, the global optimization method (GOM) is an interesting and powerful tool that assigns functions to unclassified proteins based on their positions in a physical interactions network [Vazquez, A., Flammini, A., Maritan, A. and Vespignani, A. (2003) Global protein function prediction from protein-protein interaction networks, Nat. Biotechnol., 21, 697-700]. To boost both the accuracy and speed of GOM, a new prediction method, MFGO (modified and faster global optimization) is presented in this paper, which employs local optimal repetition method to reduce calculation time, and takes account of topological structure information to achieve a more accurate prediction. On four proteins interaction datasets, including Vazquez dataset, YP dataset, DIP-core dataset, and SPK dataset, MFGO was tested and compared with the popular MR (majority rule) and GOM methods. Experimental results confirm MFGO's improvement on both speed and accuracy. Especially, MFGO m...Continue Reading

References

Apr 14, 1999·Proceedings of the National Academy of Sciences of the United States of America·M PellegriniT O Yeates
Dec 2, 2000·Nature Biotechnology·B SchwikowskiS Fields
Jul 16, 2002·Molecular & Cellular Proteomics : MCP·Charlotte M DeaneDavid Eisenberg
Jan 10, 2003·Nucleic Acids Research·Gary D BaderChristopher W V Hogue
May 13, 2003·Nature Biotechnology·Alexei VazquezAlessandro Vespignani
Feb 26, 2004·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Minghua DengFengzhu Sun
May 11, 2005·Proceedings of the National Academy of Sciences of the United States of America·Jordi EspadalerBaldomero Oliva

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Citations

Nov 23, 2006·BMC Neuroscience·Ivan ArisiVittorio Rosato
Oct 26, 2010·BMC Structural Biology·Isaac AmelaJuan Cedano
Jul 16, 2010·Cancer Informatics·Tijana MilenkovićNatasa Przulj
Oct 8, 2008·Cellular & Molecular Biology Letters·Dariusz Plewczyński, Krzysztof Ginalski
Nov 14, 2007·Journal of Computational Chemistry·Humberto González-Díaz, Francisco J Prado-Prado

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