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Journal of Integrative Bioinformatics

Editor-in-Chief: Schreiber, Falk / Hofestädt, Ralf

Managing Editor: Sommer, Björn

Ed. by Baumbach, Jan / Chen, Ming / Orlov, Yuriy / Allmer, Jens

Editorial Board: Giorgetti, Alejandro / Harrison, Andrew / Kochetov, Aleksey / Krüger, Jens / Ma, Qi / Matsuno, Hiroshi / Mitra, Chanchal K. / Pauling, Josch K. / Rawlings, Chris / Fdez-Riverola, Florentino / Romano, Paolo / Röttger, Richard / Shoshi, Alban / Soares, Siomar de Castro / Taubert, Jan / Tauch, Andreas / Yousef, Malik / Weise, Stephan / Hassani-Pak, Keywan


CiteScore 2018: 0.90

SCImago Journal Rank (SJR) 2018: 0.315

Open Access
Online
ISSN
1613-4516
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Volume 10, Issue 1

Issues

Discovery of miR-mRNA interactions via simultaneous Bayesian inference of gene networks and clusters using sequence-based predictions and expression data

Brian Godsey
Published Online: 2016-10-18 | DOI: https://doi.org/10.1515/jib-2013-227

Summary

MicroRNAs (miRs) are known to interfere with mRNA expression, and much work has been put into predicting and inferring miR-mRNA interactions. Both sequence-based interaction predictions as well as interaction inference based on expression data have been proven somewhat successful; furthermore, models that combine the two methods have had even more success. In this paper, I further refine and enrich the methods of miR-mRNA interaction discovery by integrating a Bayesian clustering algorithm into a model of prediction-enhanced miR-mRNA target inference, creating an algorithm called PEACOAT, which is written in the R language. I show that PEACOAT improves the inference of miR-mRNA target interactions using both simulated data and a data set of microarrays from samples of multiple myeloma patients. In simulated networks of 25 miRs and mRNAs, our methods using clustering can improve inference in roughly two-thirds of cases, and in the multiple myeloma data set, KEGG pathway enrichment was found to be more significant with clustering than without. Our findings are consistent with previous work in clustering of non-miR genetic networks and indicate that there could be a significant advantage to clustering of miR and mRNA expression data as a part of interaction inference.

About the article

Published Online: 2016-10-18

Published in Print: 2013-03-01


Citation Information: Journal of Integrative Bioinformatics, Volume 10, Issue 1, Pages 33–45, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2013-227.

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© 2013 The Author(s). Published by Journal of Integrative Bioinformatics.. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. BY-NC-ND 4.0

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