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 proceedingConference 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 languageEnglish
    Title of host publicationAlgebraic Biology - Second International Conference, AB 2007, Proceedings
    Pages322-333
    Number of pages12
    Volume4545 LNCS
    Publication statusPublished - 2007
    Event2nd International Conference on Algebraic Biology, AB 2007 - Castle of Hagenberg, Austria
    Duration: Jul 2 2007Jul 4 2007

    Publication series

    NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
    Volume4545 LNCS
    ISSN (Print)0302-9743
    ISSN (Electronic)1611-3349

    Other

    Other2nd International Conference on Algebraic Biology, AB 2007
    CountryAustria
    CityCastle of Hagenberg
    Period7/2/077/4/07

    Fingerprint

    Protein-protein Interaction
    Distance Matrix
    False Positive
    Proteins
    Mirrors
    Mirror
    Partial Correlation
    Coevolution
    Correlation coefficient
    Projection
    Protein
    Predict
    Prediction
    Similarity

    All Science Journal Classification (ASJC) codes

    • Theoretical Computer Science
    • Computer Science(all)

    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 (Vol. 4545 LNCS, pp. 322-333). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4545 LNCS).

    Inference of protein-protein interactions by using co-evolutionary information. / Sato, Tetsuya; Yamanishi, Yoshihiro; Horimoto, Katsuhisa; Kanehisa, Minoru; Toh, Hiroyuki.

    Algebraic Biology - Second International Conference, AB 2007, Proceedings. Vol. 4545 LNCS 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 proceedingConference 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. vol. 4545 LNCS, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 4545 LNCS, pp. 322-333, 2nd International Conference on Algebraic Biology, AB 2007, Castle of Hagenberg, Austria, 7/2/07.
    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. Vol. 4545 LNCS. 2007. p. 322-333. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
    Sato, Tetsuya ; Yamanishi, Yoshihiro ; Horimoto, Katsuhisa ; Kanehisa, Minoru ; Toh, Hiroyuki. / Inference of protein-protein interactions by using co-evolutionary information. Algebraic Biology - Second International Conference, AB 2007, Proceedings. Vol. 4545 LNCS 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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