Rank-based interolog mapping for predicting proteinprotein interactions between genomes

Yu Shu Lo, Chun Chen Chen, Kai-Cheng Hsu, Jinn Moon Yang

研究成果: 書貢獻/報告類型會議貢獻

1 引文 斯高帕斯(Scopus)

摘要

As rapidly increasing number of sequenced genomes, the methods for predicting protein-protein interactions (PPIs) from one organism to another is becoming important. Best-match and generalized interolog mapping methods have been proposed for predicting (PPIs). However, best-match mapping method suffers from low coverage of the total interactome, because of using only best matches. Generalized interolog mapping method may predict unreliable interologs at a certain similarity cutoff, because of the homologs differed in subcellular compartment, biological process, or function from the query protein. Here, we propose a new 'rank-based interolog mapping' method, which uses the pairs of proteins with high sequence similarity (E-value<10-10) and ranked by BLASTP E-value in all possible homologs to predict interologs. First, we evaluated 'rank-based interolog mapping' on predicting the PPIs in yeast. The accuracy at selecting top 5 and top 10 homologs are 0.17, and 0.12, respectively, and our method outperformed generalized interolog mapping method (accuracy=0.04) with the joint E-value<10-70. Furthermore, our method was used to predict PPIs in four organisms, including worm, fly, mouse, and human. In addition, we used Gene Ontology (GO) terms to analyzed PPIs, which reflect cellular component, biological process, and molecular function, inferred by rank-based mapping method. Our rank-based mapping method can predict more reliable interactions under a given percentage of false positives than the best-match and generalized interolog mapping methods. We believe that the rank-based mapping method is useful method for predicting PPIs in a genome-wide scale.
原文英語
主出版物標題International Conference on Systems Biology, ISB
發行者IEEE Computer Society
頁面55-62
頁數8
ISBN(列印)9781479913893
DOIs
出版狀態已發佈 - 2013
對外發佈Yes
事件2013 7th International Conference on Systems Biology, ISB 2013 - Huangshan, 中国
持續時間: 八月 23 2013八月 25 2013

其他

其他2013 7th International Conference on Systems Biology, ISB 2013
國家中国
城市Huangshan
期間8/23/138/25/13

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Computer Science Applications
  • Modelling and Simulation

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  • 引用此

    Lo, Y. S., Chen, C. C., Hsu, K-C., & Yang, J. M. (2013). Rank-based interolog mapping for predicting proteinprotein interactions between genomes. 於 International Conference on Systems Biology, ISB (頁 55-62). [6623794] IEEE Computer Society. https://doi.org/10.1109/ISB.2013.6623794