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miRNet—Functional Analysis and Visual Exploration of miRNA–Target Interactions in a Network Context

  • Yannan Fan
  • Jianguo Xia
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1819)

Abstract

To gain functional insights into microRNAs (miRNAs), researchers usually look for pathways or biological processes that are overrepresented in their target genes. The interpretation is often complicated by the fact that a single miRNA can target many genes and multiple miRNAs can regulate a single gene. Here we introduce miRNet (www.mirnet.ca), an easy-to-use web-based tool designed for creation, customization, visual exploration and functional interpretation of miRNA–target interaction networks. By integrating multiple high-quality miRNA-target data sources and advanced statistical methods into a powerful network visualization system, miRNet allows researchers to easily navigate the complex landscape of miRNA–target interactions to obtain deep biological insights. This tutorial provides a step-by-step protocol on how to use miRNet to create miRNA–target networks for visual exploration and functional analysis from different types of data inputs.

Key words

miRNA–target interaction miRNA functional analysis Network analysis Visual analytics Empirical sampling Microarray RNA-seq RT-qPCR Differential expression analysis 

Notes

Acknowledgments

The McGill Graduate Excellence Fellowship (GEF) Award (Y. Fan), the NSERC Discovery Grant, and the FRQNT New University Researcher Start-up Program grant (J. Xia) are acknowledged.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Institute of ParasitologyMcGill UniversityMontrealCanada
  2. 2.Department of Animal ScienceMcGill UniversityMontrealCanada

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