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Micro-RNA Quantification, Target Gene Identification, and Pathway Analysis

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RNA Bioinformatics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2284))

Abstract

RNA sequencing has become a powerful tool for profiling the expression level of small RNAs from both solid tissues and liquid biopsies. In conjunction with pathway analysis, it offers exciting possibilities for the identification of disease specific biomarkers. In this chapter, we describe a workflow for processing this type of sequencing data. We start by removing technical sequences (adapters) and by performing quality control, a critical task that is necessary to identify possible issues caused by sample preparation and library sequencing. We then describe read alignment and gene-level abundance estimation. Building on these results, we normalize expression profiles and compute differentially expressed microRNAs between sample groups of interest. We conclude by showing how to employ pathway analysis to identify molecular signatures corresponding to biological processes that are significantly altered by the action for microRNAs.

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Acknowledgments

This work was supported by the “My First AIRC grant” provided by Italian Association for Cancer Research to Enrica Calura (MFAG 2019, number 23522).

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Authors and Affiliations

  1. Department of Biology, University of Padova, Padova, Italy

    Gabriele Sales & Enrica Calura

Authors
  1. Gabriele Sales
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  2. Enrica Calura
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Corresponding author

Correspondence to Gabriele Sales .

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Editors and Affiliations

  1. Dipartimento Di Bioscienze Biotecnologie E Biofarmaceutica, Università degli Studi di Bari Aldo Moro, Bari, Italy

    Ernesto Picardi

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Sales, G., Calura, E. (2021). Micro-RNA Quantification, Target Gene Identification, and Pathway Analysis. In: Picardi, E. (eds) RNA Bioinformatics. Methods in Molecular Biology, vol 2284. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1307-8_12

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  • DOI: https://doi.org/10.1007/978-1-0716-1307-8_12

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1306-1

  • Online ISBN: 978-1-0716-1307-8

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