TransDomain: A transitive domain-based method in protein-protein interaction prediction

Yi Tsung Tang, Hung Yu Kao

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

The prediction of new protein-protein interactions is important due to many unknown functions of biological pathways. In addition, many protein-protein interaction databases contain different types of protein interactions, i.e., protein associations, physical protein associations and direct protein interactions. Moreover, discovering new crucial protein-protein interactions through biological experiments is still difficult. Therefore, there is increasing demand to discover not only protein associations but also direct protein interactions. Many studies have predicted protein-protein interactions by directly using biological features, such as Gene Ontology (GO) functions and domains of protein structure between two interacting proteins. In this article, we propose TransDomain, a new method of predicting potential protein-protein interactions by using a new strong transitive relationship between interacting protein domains. Our results demonstrate that TransDomain can effectively predict potential protein-protein interactions from existing identified protein interaction relationships. TransDomain achieved 90% precision rate and 91% accuracy in the prediction of all types of protein-protein interactions and outperformed the existing PPI prediction systems and simulated GO-based prediction methods.

Original languageEnglish
Title of host publicationBioinformatics Research and Applications - 7th International Symposium, ISBRA 2011, Proceedings
Pages240-252
Number of pages13
DOIs
Publication statusPublished - 2011 May 16
Event7th International Symposium on Bioinformatics Research and Applications, ISBRA 2011 - Changsha, China
Duration: 2011 May 272011 May 29

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume6674 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other7th International Symposium on Bioinformatics Research and Applications, ISBRA 2011
CountryChina
CityChangsha
Period11-05-2711-05-29

    Fingerprint

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

Tang, Y. T., & Kao, H. Y. (2011). TransDomain: A transitive domain-based method in protein-protein interaction prediction. In Bioinformatics Research and Applications - 7th International Symposium, ISBRA 2011, Proceedings (pp. 240-252). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 6674 LNBI). https://doi.org/10.1007/978-3-642-21260-4_24