MicroRNA target identification : methods and protocols

Author(s)

    • Laganà, Alessandro

Bibliographic Information

MicroRNA target identification : methods and protocols

edited by Alessandro Laganà

(Methods in molecular biology / John M. Walker, series editor, v. 1970)(Springer protocols)

Humana Press, c2019

Available at  / 1 libraries

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Note

Includes bibliographical references and index

Description and Table of Contents

Description

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.

Table of Contents

1. A Practical Guide to miRNA Target Prediction Most Mauluda Akhtar, Luigina Micolucci, Md Soriful Islam, Fabiola Olivieri, and Antonio Domenico Procopio 2. miRandb: A Meta-Database of Online Resources of miRNA and miRNA Targets Seyed Hamid Aghaee-Bakhtiari 3. Sfold Tools for MicroRNA Target Prediction William Rennie, Shaveta Kanoria, Chaochun Liu, C. Steven Carmack, Jun Lu, and Ye Ding 4. The Role of Tertiary Structure in MicroRNA Target Recognition Hin Hark Gan and Kristin C. Gunsalus 5. Protocols for miRNA Target Prediction in Plants Gaurav Sablok, Kun Yang, and Xiaopen Wen 6. Improving miRNA-Target Prediction Using CLASH Data Xiaoman Li and Haiyan Hu 7. Integration of Omics Data to Identify Cancer-Related MicroRNA Luciano Cascione 8. Functional Analysis of Genetic Variants and Somatic Mutations Impacting MicroRNA-Target Recognition: Bioinformatics Resources Jesse D. Ziebarth, Anindya Bhattacharya, and Yan Cui 9. Construction and Analysis of miRNA Regulatory Networks Antonella Mensi, Vincenzo Bonnici, Simone Caligola, and Rosalba Giugno 10. Identification of Disease-miRNA Networks across Different Cancer Types Using SWitchMiner (SWIM) Giulia Fiscon, Federica Conte, Lorenzo Farina, Marco Pellegrini, Francesco Russo, and Paola Paci 11. Computational Methods to Investigate the Impact of miRNAs on Pathways Salvatore Alaimo, Giovanni Micale, Alessandro La Ferlita, Alfredo Ferro, and Alfredo Pulvirenti 12. Consensus Target Prediction with Enrichment Analysis for MicroRNAs Harboring Editing Sites and Other Variations Giovanni Nigita, Rosario Distefano, Dario Veneziano, Giulia Romano, Mario Acunzo, and Carlo M. Croce 13. A Roadmap for the Computational Prediction and Experimental Validation of Competitive Endogenous RNAs Florian A. Karreth 14. Investigating miRNA-lncRNA Interactions: Computational Tools and Resources Dario Veneziano, Gioacchino P. Marceca, Sebastiano Di Bella, Giovanni Nigita, Rosario Distefano, and Carlo M. Croce 15. Combing the Hairball: Improving Visualization of miRNA-Target Interaction Networks Francesco Russo, Jessica Xin Hu, Jose Alejandro Romero Herrera, and Soren Brunak 16. Inconsistencies and Limitations of Current MicroRNA Target Identification Methods Sophie Mockly and Herve Seitz 17. Experimental Validation of MicroRNA Targets: Luciferase Reporter Assay Luisa Tomasello, Landon Cluts, and Carlo M. Croce 18. Experimental Validation of MicroRNA Targets: Mutagenesis of the Binding Regions Luisa Tomasello, Landon Cluts, and Carlo M. Croce 19. Experimental Validation of MicroRNA Targets: Analysis of MicroRNA Targets through Western Blotting Luisa Tomasello, Landon Cluts, and Carlo M. Croce

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