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Bioinformatics Advance Access published online on June 9, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti532
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received October 14, 2004
Revised May 13, 2005
Accepted June 7, 2005

Article

Refined phylogenetic profiles method for predicting protein-protein interactions

Jingchun Sun 1, Jinlin Xu 1, Zhen Liu 2, Qi Liu 3, Aimin Zhao 4, Tieliu Shi 3, and Yixue Li 3*

1 School of Life Sciences & Technology, Shanghai Jiaotong University, Shanghai, 200240, China
2 Department of Biology, Hunan Normal University, Changsha, 410081, China
3 Bioinformation Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
4 The Chinese National Center for Biotechnology Development, Beijing 100081, China

* To whom correspondence should be addressed.
Yixue Li, E-mail: yxli{at}sibs.ac.cn


  Abstract

Motivation: The increasing availability of complete genome sequences provides excellent opportunity for further developing tools for functional studies in proteomics. Several experimental approaches and in silico algorithms have been developed to cluster proteins into networks of biological significance that may provide new biological insights, especially into understanding the functions of many uncharacterized proteins. Among these methods, the phylogenetic profiles method has been widely used to predict protein-protein interactions. It involves the selection of reference organisms and identification of homologous proteins. Up to now, no published report has systematically studied the effects of the reference genome selection and the identification of homologous proteins upon the accuracy of this method.

Results: In this study, we optimized the phylogenetic profiles method by integrating phylogenetic relationships among reference organisms and sequence homology information to improve prediction accuracy. Our results revealed that the selection of reference organisms set and the criteria for homology identification significantly are two critical factors for the prediction accuracy of this method. Our refined phylogenetic profiles method shows greater performance and potentially provides more reliable functional linkages compared to previous methods.

Availability: The software (C, Perl) is available from the corresponding author.

Supplementary Information: There are three supplementary materials online, including related materials and results.


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