Rank-based interolog mapping for predicting proteinprotein interactions between genomes

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

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

1 Citation (Scopus)

Abstract

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) 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-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.

Original languageEnglish
Title of host publicationInternational Conference on Systems Biology, ISB
PublisherIEEE Computer Society
Pages55-62
Number of pages8
ISBN (Print)9781479913893
DOIs
Publication statusPublished - 2013
Externally publishedYes
Event2013 7th International Conference on Systems Biology, ISB 2013 - Huangshan, China
Duration: Aug 23 2013Aug 25 2013

Other

Other2013 7th International Conference on Systems Biology, ISB 2013
CountryChina
CityHuangshan
Period8/23/138/25/13

Fingerprint

Protein-protein Interaction
Genome
Genes
Proteins
Biological Phenomena
Predict
Protein
Gene Ontology
Worm
Yeast
False Positive
Diptera
Ontology
Percentage
Mouse
Coverage
Joints
Yeasts

Keywords

  • interolog mapping
  • Rank-based strategy

ASJC Scopus subject areas

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

Cite this

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

Rank-based interolog mapping for predicting proteinprotein interactions between genomes. / Lo, Yu Shu; Chen, Chun Chen; Hsu, Kai-Cheng; Yang, Jinn Moon.

International Conference on Systems Biology, ISB. IEEE Computer Society, 2013. p. 55-62 6623794.

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

Lo, YS, Chen, CC, Hsu, K-C & Yang, JM 2013, Rank-based interolog mapping for predicting proteinprotein interactions between genomes. in International Conference on Systems Biology, ISB., 6623794, IEEE Computer Society, pp. 55-62, 2013 7th International Conference on Systems Biology, ISB 2013, Huangshan, China, 8/23/13. https://doi.org/10.1109/ISB.2013.6623794
Lo YS, Chen CC, Hsu K-C, Yang JM. Rank-based interolog mapping for predicting proteinprotein interactions between genomes. In International Conference on Systems Biology, ISB. IEEE Computer Society. 2013. p. 55-62. 6623794 https://doi.org/10.1109/ISB.2013.6623794
Lo, Yu Shu ; Chen, Chun Chen ; Hsu, Kai-Cheng ; Yang, Jinn Moon. / Rank-based interolog mapping for predicting proteinprotein interactions between genomes. International Conference on Systems Biology, ISB. IEEE Computer Society, 2013. pp. 55-62
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