Protein complex detection in PPI networks based on data integration and supervised learning method

BMC Bioinformatics
Feng YuJian Wang

Abstract

Revealing protein complexes are important for understanding principles of cellular organization and function. High-throughput experimental techniques have produced a large amount of protein interactions, which makes it possible to predict protein complexes from protein-protein interaction (PPI) networks. However, the small amount of known physical interactions may limit protein complex detection. The new PPI networks are constructed by integrating PPI datasets with the large and readily available PPI data from biomedical literature, and then the less reliable PPI between two proteins are filtered out based on semantic similarity and topological similarity of the two proteins. Finally, the supervised learning protein complex detection (SLPC), which can make full use of the information of available known complexes, is applied to detect protein complex on the new PPI networks. The experimental results of SLPC on two different categories yeast PPI networks demonstrate effectiveness of the approach: compared with the original PPI networks, the best average improvements of 4.76, 6.81 and 15.75 percentage units in the F-score, accuracy and maximum matching ratio (MMR) are achieved respectively; compared with the denoising PPI networks...Continue Reading

References

Dec 26, 2001·Nucleic Acids Research·Selina S DwightJ Michael Cherry
Mar 28, 2002·Nucleic Acids Research·A J EnrightC A Ouzounis
Jan 15, 2003·BMC Bioinformatics·Gary D Bader, Christopher W V Hogue
Dec 19, 2003·Nucleic Acids Research·H W MewesA Ruepp
Mar 27, 2004·Science·Patrick AloyRobert B Russell
Jan 24, 2006·Nature·Anne-Claude GavinGiulio Superti-Furga
Feb 14, 2006·Bioinformatics·Balázs AdamcsekTamás Vicsek
Mar 24, 2006·Nature·Nevan J KroganJack F Greenblatt
May 27, 2006·Molecular Systems Biology·Aimée Marie DudleyGeorge McDonald Church
Nov 8, 2006·BMC Bioinformatics·Sylvain Brohée, Jacques van Helden
Dec 7, 2006·Genome Biology·G Traver HartEdward M Marcotte
Jul 1, 2008·Bioinformatics·Yanjun QiZiv Bar-Joseph
May 14, 2009·Bioinformatics·Guimei LiuHon Nian Chua
Jun 3, 2009·BMC Bioinformatics·Min WuSee-Kiong Ng
Sep 22, 2009·Journal of Proteome Research·Lei ChenYu-Dong Cai
Mar 20, 2012·Nature Methods·Tamás NepuszAlberto Paccanaro
Aug 27, 2013·IEEE Transactions on Nanobioscience·Zhihao YangHongfei Lin

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Software Mentioned

MCODE
MIPS
PPIExtractor
Cfinder
ClusterONE
Aloy
MCL
COACH
SLPC
TAP06

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