DIANA‐TarBase and DIANA Suite Tools: Studying Experimentally Supported microRNA Targets

Maria D. Paraskevopoulou1, Ioannis S. Vlachos1, Artemis G. Hatzigeorgiou1

1 Hellenic Pasteur Institute, Athens
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 12.14
DOI:  10.1002/cpbi.12
Online Posting Date:  September, 2016
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Abstract

microRNAs (miRNAs) are short non‐coding RNAs (∼22 nts) present in animals, plants, and viruses. They are considered central post‐transcriptional regulators of gene expression and are key components in a great number of physiological and pathological conditions. The accurate characterization of their targets is considered essential to a series of applications and basic or applied research settings. DIANA‐TarBase (http://www.microrna.gr/tarbase) was initially launched in 2006. It is a reference repository indexing experimentally derived miRNA‐gene interactions in different cell types, tissues, and conditions across numerous species. This unit focuses on the study of experimentally supported miRNA‐gene interactions, as well as their functional interpretation through the use of available tools in the DIANA suite (http://www.microrna.gr). The proposed use‐case scenarios are presented in protocols, describing how to utilize the DIANA‐TarBase database and DIANA‐microT‐CDS server and perform miRNA‐targeted pathway analysis with DIANA‐miRPath‐v3. All analyses are directly invoked or initiated from DIANA‐TarBase. © 2016 by John Wiley & Sons, Inc.

Keywords: microRNA; target; interaction; experimental methodology; high‐throughput; pathway; in silico predictions; RNAi; miRNA interactome

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Querying DIANA‐TarBase
  • Basic Protocol 2: Identifying In Silico–Predicted miRNA TARGETS Using Diana‐microT‐CDS
  • Basic Protocol 3: Querying DIANA‐miRPath v3.0
  • Support Protocol 1: Saving Queries in a DIANA‐Tools Account
  • Guidelines for Understanding Results
  • Acknowledgements
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

Basic Protocol 1: Querying DIANA‐TarBase

  Necessary Resources
  • Essential prerequisites are a Windows, Linux, Unix, or MacOS environment, as well as an installed up‐to‐date Web browser

Basic Protocol 2: Identifying In Silico–Predicted miRNA TARGETS Using Diana‐microT‐CDS

  Necessary Resources
  • Essential prerequisites are a Windows, Linux, Unix, or MacOS environment, as well as an installed up‐to‐date Web browser. Downloaded files are in text (.csv) format and therefore require applications (text editor or spreadsheet application) for further processing.

Basic Protocol 3: Querying DIANA‐miRPath v3.0

  Necessary Resources
  • Essential prerequisites are a Windows, Linux, Unix, or MacOS environment, as well as an installed up‐to‐date Web browser. Downloaded files are in text (.csv) format and therefore require applications (text editor or spreadsheet application) for further processing.

Support Protocol 1: Saving Queries in a DIANA‐Tools Account

  Necessary Resources
  • Essential prerequisites are a Windows, Linux, Unix, or MacOS environment, as well as an installed up‐to‐date Web browser
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Figures

Videos

Literature Cited

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