An accessibility-incorporated method for accurate prediction of RNA-RNA interactions from sequence data

Yuki Kato, Tomoya Mori, Kengo Sato, Shingo Maegawa, Hiroshi Hosokawa, Tatsuya Akutsu

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Motivation: RNA-RNA interactions via base pairing play a vital role in the post-transcriptional regulation of gene expression. Efficient identification of targets for such regulatory RNAs needs not only discriminative power for positive and negative RNA-RNA interacting sequence data but also accurate prediction of interaction sites from positive data. Recently, a few studies have incorporated interaction site accessibility into their prediction methods, indicating the enhancement of predictive performance on limited positive data. Results: Here we show the efficacy of our accessibility-based prediction model RactIPAce on newly compiled datasets. The first experiment in interaction site prediction shows that RactIPAce achieves the best predictive performance on the newly compiled dataset of experimentally verified interactions in the literature as compared with the state-of-the-art methods. In addition, the second experiment in discrimination between positive and negative interacting pairs reveals that the combination of accessibility-based methods including our approach can be effective to discern real interacting RNAs. Taking these into account, our prediction model can be effective to predict interaction sites after screening for real interacting RNAs, which will boost the functional analysis of regulatory RNAs.

Original languageEnglish
Pages (from-to)202-209
Number of pages8
JournalBioinformatics
Volume33
Issue number2
DOIs
Publication statusPublished - 2017 Jan 15

Fingerprint

RNA
Accessibility
Prediction
Interaction
Prediction Model
Transcriptional Regulation
Functional Analysis
Pairing
Gene Expression Regulation
Functional analysis
Discrimination
Gene Expression
Experiment
Screening
Efficacy
Base Pairing
Enhancement
Gene expression
Predict
Target

ASJC Scopus subject areas

  • Statistics and Probability
  • Medicine(all)
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

An accessibility-incorporated method for accurate prediction of RNA-RNA interactions from sequence data. / Kato, Yuki; Mori, Tomoya; Sato, Kengo; Maegawa, Shingo; Hosokawa, Hiroshi; Akutsu, Tatsuya.

In: Bioinformatics, Vol. 33, No. 2, 15.01.2017, p. 202-209.

Research output: Contribution to journalArticle

Kato, Yuki ; Mori, Tomoya ; Sato, Kengo ; Maegawa, Shingo ; Hosokawa, Hiroshi ; Akutsu, Tatsuya. / An accessibility-incorporated method for accurate prediction of RNA-RNA interactions from sequence data. In: Bioinformatics. 2017 ; Vol. 33, No. 2. pp. 202-209.
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