Inference of protein-protein interactions by using co-evolutionary information

Tetsuya Sato; Yoshihiro Yamanishi; Katsuhisa Horimoto; Minoru Kanehisa; Hiroyuki Toh

doi:10.1007/978-3-540-73433-8_23

Inference of protein-protein interactions by using co-evolutionary information

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

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Abstract

The mirror tree is a method to predict protein-protein interaction by evaluating the similarity between distance matrices of proteins. It is known, however, that predictions by the mirror tree method include many false positives. We suspected that the information about the evolutionary relationship of source organisms may be the cause of the false positives, because the information is shared by the distance matrices. Therefore, we excluded the information from the distance matrices and evaluated the similarity of the residuals as the intensity of co-evolution. We developed two different methods with a projection operation and partial correlation coefficient. The number of false positives were drastically reduced by our methods.

Original language	English
Title of host publication	Algebraic Biology - Second International Conference, AB 2007, Proceedings
Publisher	Springer Verlag
Pages	322-333
Number of pages	12
ISBN (Print)	9783540734321
DOIs	https://doi.org/10.1007/978-3-540-73433-8_23
Publication status	Published - 2007
Externally published	Yes
Event	2nd International Conference on Algebraic Biology, AB 2007 - Castle of Hagenberg, Austria Duration: Jul 2 2007 → Jul 4 2007

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	4545 LNCS
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Other

Other	2nd International Conference on Algebraic Biology, AB 2007
Country/Territory	Austria
City	Castle of Hagenberg
Period	7/2/07 → 7/4/07

All Science Journal Classification (ASJC) codes

Theoretical Computer Science
Computer Science(all)

Access to Document

10.1007/978-3-540-73433-8_23

Cite this

Sato, T., Yamanishi, Y., Horimoto, K., Kanehisa, M., & Toh, H. (2007). Inference of protein-protein interactions by using co-evolutionary information. In Algebraic Biology - Second International Conference, AB 2007, Proceedings (pp. 322-333). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4545 LNCS). Springer Verlag. https://doi.org/10.1007/978-3-540-73433-8_23

Inference of protein-protein interactions by using co-evolutionary information. / Sato, Tetsuya; Yamanishi, Yoshihiro; Horimoto, Katsuhisa et al.
Algebraic Biology - Second International Conference, AB 2007, Proceedings. Springer Verlag, 2007. p. 322-333 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4545 LNCS).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Sato, T, Yamanishi, Y, Horimoto, K, Kanehisa, M & Toh, H 2007, Inference of protein-protein interactions by using co-evolutionary information. in Algebraic Biology - Second International Conference, AB 2007, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 4545 LNCS, Springer Verlag, pp. 322-333, 2nd International Conference on Algebraic Biology, AB 2007, Castle of Hagenberg, Austria, 7/2/07. https://doi.org/10.1007/978-3-540-73433-8_23

Sato T, Yamanishi Y, Horimoto K, Kanehisa M, Toh H. Inference of protein-protein interactions by using co-evolutionary information. In Algebraic Biology - Second International Conference, AB 2007, Proceedings. Springer Verlag. 2007. p. 322-333. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-540-73433-8_23

Sato, Tetsuya ; Yamanishi, Yoshihiro ; Horimoto, Katsuhisa et al. / Inference of protein-protein interactions by using co-evolutionary information. Algebraic Biology - Second International Conference, AB 2007, Proceedings. Springer Verlag, 2007. pp. 322-333 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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abstract = "The mirror tree is a method to predict protein-protein interaction by evaluating the similarity between distance matrices of proteins. It is known, however, that predictions by the mirror tree method include many false positives. We suspected that the information about the evolutionary relationship of source organisms may be the cause of the false positives, because the information is shared by the distance matrices. Therefore, we excluded the information from the distance matrices and evaluated the similarity of the residuals as the intensity of co-evolution. We developed two different methods with a projection operation and partial correlation coefficient. The number of false positives were drastically reduced by our methods.",

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AB - The mirror tree is a method to predict protein-protein interaction by evaluating the similarity between distance matrices of proteins. It is known, however, that predictions by the mirror tree method include many false positives. We suspected that the information about the evolutionary relationship of source organisms may be the cause of the false positives, because the information is shared by the distance matrices. Therefore, we excluded the information from the distance matrices and evaluated the similarity of the residuals as the intensity of co-evolution. We developed two different methods with a projection operation and partial correlation coefficient. The number of false positives were drastically reduced by our methods.

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Inference of protein-protein interactions by using co-evolutionary information

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