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

J Integr Bioinform. 2013 Jul 10;10(1):227. doi: 10.2390/biecoll-jib-2013-227.

Abstract

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 miRmRNA 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.

MeSH terms

  • Base Sequence
  • Bayes Theorem
  • Cluster Analysis
  • Computational Biology / methods*
  • Computer Simulation
  • Databases, Genetic
  • Gene Expression Regulation, Neoplastic*
  • Gene Regulatory Networks / genetics*
  • Humans
  • MicroRNAs / genetics
  • MicroRNAs / metabolism*
  • Multiple Myeloma / genetics
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism*
  • ROC Curve
  • Signal Transduction / genetics

Substances

  • MicroRNAs
  • RNA, Messenger