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Sequence and Genome Analysis: Methods and Applications
Title
Sequence and Genome Analysis: Methods and Applications
Editor
Zhongming Zhao
Price
USD$149.00
ISBN
978-1-453753-859
Clicks
35111

Chapter 8

Sequence and Genome Analysis: Methods and Applications

Improvement of the mirrortree method by extracting evolutionary information

by Tetsuya Sato, Yoshihiro Yamanishi, Minoru Kanehisa, Katsuhisa Horimoto and Hiroyuki Toh

Viewed: 2774

Abstract

The prediction of protein–protein interactions is one of the major issues of bioinformatics. Recently, a variety of co-evolution-based methods have been developed for this goal. Mirrortree is one of such methods, which has been independently developed by Goh et al., (2000) and Pazos and Valencia (2001). In the mirrortree method, a correlation coefficient between the distance matrices of a pair of proteins under consideration is calculated as the intensity of co-evolution. High correlation is considered to indicate the interaction of the proteins. Due to the simplicity of the method, mirrortree is widely utilized for the theoretical analysis of protein-protein interactions. However, it is known that the predictions by the mirrortree method include many false positives. We suspected that the information about the evolutionary relationship among the source organisms shared by distance matrices might be the cause of the false positives. Therefore, we have developed two methods to exclude such information from the distance matrices. In these methods, the intensity of co-evolution is evaluated as the correlation coefficient between the residuals of the exclusion. One of the methods uses a projection operation to exclude the evolutionary information from the distance matrices, whereas partial correlation coefficient is used in the other method for the exclusion. Both methods can drastically reduce false positives to increase the specificity, comparing to the original mirrortree prediction. However, sensitivity is decreased in our approach due to the increase of false negatives. Several groups have also developed the methods similar to our approach. The similarity and difference among the methods, together with recent trend of mirrortree approach, will be discussed.

Author Details

Tetsuya Sato
Kyushu University
Yoshihiro Yamanishi
Ecole des Mines de Paris
Minoru Kanehisa
Kyoto University
Katsuhisa Horimoto
National Institute of Advanced Industrial Science
Hiroyuki Toh
Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Japan, Japan

Citation

Tetsuya Sato, Yoshihiro Yamanishi, Minoru Kanehisa, Katsuhisa Horimoto and Hiroyuki Toh. Improvement of the mirrortree method by extracting evolutionary information. In Sequence and Genome Analysis: Methods and Applications. ISBN:978-1-453753-859. iConcept Press. 0000.

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