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Surveying computational algorithms for identification of miRNA–mRNA regulatory modules

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Abstract

MicroRNAs (miRNAs) are small non-coding RNA that target gene expression at post-transcriptional level. To understand the molecular basis of miRNA regulation, it is essential to identify reliable miRNA target mRNAs and miRNA–mRNA functional networks. Several computational algorithms and tools are widely used for discovering miRNA–mRNA regulatory modules. We have comprehensively reviewed thirty-two tools and databases that were developed over the past decade. Our in-depth survey considers all significant features including underlying methodologies in each tool for basis of miRNA–mRNA functional module discovery. Current miRNA–mRNA functional module identification tools utilizes sequence based prediction, graph theory combined with Bayesian network, probabilistic and rule learning methods. Further we discuss ease of use, availability, and suitability of these methods, and provide an overview of recent computational algorithms used in miRNA–mRNA regulatory module identification.

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Acknowledgements

This work is supported by National Institute of Biomedical Genomics, Kalyani.

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Authors and Affiliations

  1. National Institute of Biomedical Genomics, P.O.: N.S.S., Kalyani, West-Bengal, 741251, India

    Rishav Ray & Priyanka Pandey

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  1. Rishav Ray
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  2. Priyanka Pandey
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Correspondence to Priyanka Pandey.

Additional information

This article is based on the presentation made during the 17th All India Congress of Cytology and Genetics and International Symposium on “Exploring Genomes: The New Frontier” held at CSIR-Indian Institute of Chemical biology Kolkata in collaboration with Archana Sharma Foundation of Calcutta during December 22–24 2015.

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Ray, R., Pandey, P. Surveying computational algorithms for identification of miRNA–mRNA regulatory modules. Nucleus 60, 165–174 (2017). https://doi.org/10.1007/s13237-017-0208-5

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  • DOI: https://doi.org/10.1007/s13237-017-0208-5

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