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Identification of RNAs Engaged in Direct RNA-RNA Interaction with a Long Non-Coding RNA
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Constructing prediction models from expression profiles for large scale lncRNA-miRNA interaction profiling.

Yu-An Huang1, Keith C C Chan1, Zhu-Hong You1,2

  • 1Department of Computing, Hong Kong Polytechnic University, Hong Kong.

Bioinformatics (Oxford, England)
|October 26, 2017
PubMed
Summary
This summary is machine-generated.

This study introduces EPLMI, a computational method to predict long non-coding RNA (lncRNA) and microRNA (miRNA) interactions. EPLMI effectively identifies interaction patterns, aiding research into gene regulation and ceRNA networks.

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Area of Science:

  • Computational biology
  • Genomics
  • Molecular biology

Background:

  • MicroRNA (miRNA) and long non-coding RNA (lncRNA) interactions are crucial for gene regulation.
  • Limited computational tools exist for analyzing and predicting these interactions.
  • Evidence suggests lncRNA-miRNA interactions are linked to expression levels via a titration mechanism.

Purpose of the Study:

  • To develop a computational approach for analyzing and predicting lncRNA-miRNA interactions.
  • To investigate patterns in large-scale expression profiles of known lncRNA-miRNA interactions.
  • To leverage identified patterns for a novel prediction model.

Main Methods:

  • Represented known lncRNA-miRNA interactions as a bipartite graph.
  • Developed the EPLMI technique to construct a prediction model from this graph.
  • Assumed similar lncRNAs exhibit similar interaction patterns with miRNAs, and vice versa.

Main Results:

  • The EPLMI model achieved high prediction accuracy, with AUCs of 0.8522 (LOOCV) and 0.8447 ± 0.0017 (5-fold CV).
  • Demonstrated reliable prediction of lncRNA-miRNA interactions.
  • Showcased the model's utility in identifying potential lncRNA targets for specific miRNAs.

Conclusions:

  • EPLMI provides a reliable method for large-scale lncRNA-miRNA interaction profiling.
  • The prediction models generated by EPLMI can offer significant insights into ceRNA regulatory networks.
  • EPLMI is the first technique developed for comprehensive lncRNA-miRNA interaction profiling.