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MicroRNA Target Identification

Methods and Protocols

  • Book
  • © 2019

Overview

Editors:
  1. Alessandro Laganà

    1. Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, USA

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  • Includes cutting-edge techniques
  • Provides step-by-step detail essential for reproducible results
  • Contains key implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1970)

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Table of contents (19 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. A Practical Guide to miRNA Target Prediction

    • Most Mauluda Akhtar, Luigina Micolucci, Md Soriful Islam, Fabiola Olivieri, Antonio Domenico Procopio
    Pages 1-13

  3. miRandb: A Metadatabase of Online Resources of miRNA and miRNA Targets

    • Seyed Hamid Aghaee-Bakhtiari
    Pages 15-30

  4. Sfold Tools for MicroRNA Target Prediction

    • William Rennie, Shaveta Kanoria, Chaochun Liu, C. Steven Carmack, Jun Lu, Ye Ding
    Pages 31-42

  5. The Role of Tertiary Structure in MicroRNA Target Recognition

    • Hin Hark Gan, Kristin C. Gunsalus
    Pages 43-64

  6. Protocols for miRNA Target Prediction in Plants

    • Gaurav Sablok, Kun Yang, Xiaopeng Wen
    Pages 65-73

  7. Improving miRNA Target Prediction Using CLASH Data

    • Xiaoman Li, Haiyan Hu
    Pages 75-83

  8. Integration of Omics Data to Identify Cancer-Related MicroRNA

    • Luciano Cascione
    Pages 85-99

  9. Functional Analysis of Genetic Variants and Somatic Mutations Impacting MicroRNA-Target Recognition: Bioinformatics Resources

    • Jesse D. Ziebarth, Anindya Bhattacharya, Yan Cui
    Pages 101-120

  10. Construction and Analysis of miRNA Regulatory Networks

    • Antonella Mensi, Vincenzo Bonnici, Simone Caligola, Rosalba Giugno
    Pages 121-167

  11. Identification of Disease–miRNA Networks Across Different Cancer Types Using SWIM

    • Giulia Fiscon, Federica Conte, Lorenzo Farina, Marco Pellegrini, Francesco Russo, Paola Paci
    Pages 169-181

  12. Computational Methods to Investigate the Impact of miRNAs on Pathways

    • Salvatore Alaimo, Giovanni Micale, Alessandro La Ferlita, Alfredo Ferro, Alfredo Pulvirenti
    Pages 183-209

  13. isoTar: Consensus Target Prediction with Enrichment Analysis for MicroRNAs Harboring Editing Sites and Other Variations

    • Rosario Distefano, Giovanni Nigita, Dario Veneziano, Giulia Romano, Carlo M. Croce, Mario Acunzo
    Pages 211-235

  14. A Roadmap for the Computational Prediction and Experimental Validation of Competitive Endogenous RNAs

    • Florian A. Karreth
    Pages 237-250

  15. Investigating miRNA–lncRNA Interactions: Computational Tools and Resources

    • Dario Veneziano, Gioacchino P. Marceca, Sebastiano Di Bella, Giovanni Nigita, Rosario Distefano, Carlo M. Croce
    Pages 251-277

  16. Combing the Hairball: Improving Visualization of miRNA–Target Interaction Networks

    • Francesco Russo, Jessica Xin Hu, Jose Alejandro Romero Herrera, Søren Brunak
    Pages 279-289

  17. Inconsistencies and Limitations of Current MicroRNA Target Identification Methods

    • Sophie Mockly, Hervé Seitz
    Pages 291-314

  18. Experimental Validation of MicroRNA Targets: Luciferase Reporter Assay

    • Luisa Tomasello, Landon Cluts, Carlo M. Croce
    Pages 315-330

  19. Experimental Validation of MicroRNA Targets: Mutagenesis of Binding Regions

    • Luisa Tomasello, Landon Cluts, Carlo M. Croce
    Pages 331-339

  20. Experimental Validation of MicroRNA Targets: Analysis of MicroRNA Targets Through Western Blotting

    • Luisa Tomasello, Landon Cluts, Carlo M. Croce
    Pages 341-353
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Keywords

About this book

This detailed book provides a comprehensive state-of-the-art presentation of all aspects of miRNA target identification, from the prediction of miRNA binding sites on their target molecules to their experimental validation and downstream functional analysis. It also explores methodologies and tools for target prediction and related analysis, as well as tutorials on specific tasks, tools, and analysis pipelines. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. 

Authoritative and practical, MicroRNA Target Identification: Methods and Protocols updates on basic and advanced concepts involving miRNA target identification and delivers an extremely useful guide to specific computational tasks and analysis in miRNA research.

Editors and Affiliations

  • Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, USA

    Alessandro Laganà

Bibliographic Information

  • Book Title: MicroRNA Target Identification

  • Book Subtitle: Methods and Protocols

  • Editors: Alessandro Laganà

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-9207-2

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2019

  • Hardcover ISBN: 978-1-4939-9206-5Published: 09 April 2019

  • eBook ISBN: 978-1-4939-9207-2Published: 08 April 2019

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 359

  • Number of Illustrations: 17 b/w illustrations, 102 illustrations in colour

  • Topics: Human Genetics

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