Obtaining miRNA‐Target Interaction Information from miRWalk2.0

Alisha Parveen1, Norbert Gretz1, Harsh Dweep1

1 Medical Research Center, Medical Faculty of Mannheim, University of Heidelberg, Mannheim
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 12.15
DOI:  10.1002/cpbi.14
Online Posting Date:  September, 2016
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Abstract

miRWalk2.0 (http://zmf.umm.uni‐heidelberg.de/mirwalk2) is a freely accessible, regularly updated comprehensive archive supplying the largest available collection of predicted and experimentally verified miRNA‐target interactions, with various novel and unique features to assist the scientific community. Approximately 949 million interactions between 11,748 miRNAs, 308,700 genes, and 68,460 lncRNAs are documented in miRWalk2.0 with 5,146,217 different kinds of identifiers to offer a one‐stop site to collect an abundance of information. This article describes a schematic workflow on how to obtain miRNA‐target interactions from miRWalk2.0. © 2016 by John Wiley & Sons, Inc.

Keywords: micro RNA; miRNA; database; miRWalk2.0; target predictions; pathways; gene ontologies

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Retrieving Predicted miRNA‐Target Interactions Using the PTM of miRWalk2.0
  • Basic Protocol 2: Retrieving Experimentally Verified miRNA‐Target Interactions Using the VTM of miRWalk2.0
  • Alternate Protocol 1: Holistic view of Gene‐miRNA Interactions or Download Page
  • Alternate Protocol 2: Customized Gene Set Builder System for miRNA
  • Guidelines for Understanding Results
  • Predicted Target Module
  • Validated Target Module
  • Commentary
  • Figures
     
 
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Materials

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Figures

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Literature Cited

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Internet Resources
  http://zmf.umm.uni‐heidelberg.de/apps/zmf/mirwalk2/documentation.html#pathtar
  Information about the resources used to collate data sets on genes, miRNAs, biological signaling cascades and putative as well as experimentally verified miRNA‐target interaction.
  http://zmf.umm.uni‐heidelberg.de/apps/zmf/mirwalk2/documentation.html#chrotar
  A complete list of databases that have been hyperlinked to annotate the result pages of miRWalk2.0.
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