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Microarray-Based MicroRNA Expression Data Analysis with Bioconductor

  • Emilio Mastriani
  • Rihong Zhai
  • Songling Zhu
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1751)

Abstract

MicroRNAs (miRNAs) are small, noncoding RNAs that are able to regulate the expression of targeted mRNAs. Thousands of miRNAs have been identified; however, only a few of them have been functionally annotated. Microarray-based expression analysis represents a cost-effective way to identify candidate miRNAs that correlate with specific biological pathways, and to detect disease-associated molecular signatures. Generally, microarray-based miRNA data analysis contains four major steps: (1) quality control and normalization, (2) differential expression analysis, (3) target gene prediction, and (4) functional annotation. For each step, a large couple of software tools or packages have been developed. In this chapter, we present a standard analysis pipeline for miRNA microarray data, assembled by packages mainly developed with R and hosted in Bioconductor project.

Key words

MicroRNA (miRNA) Bioconcductor R Package Gene expression analysis Microarray data analysis 

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Copyright information

© Springer Science+Business Media, LLC 2018

Authors and Affiliations

  • Emilio Mastriani
    • 1
    • 2
  • Rihong Zhai
    • 3
  • Songling Zhu
    • 1
    • 2
  1. 1.Systemomics Center, College of PharmacyHarbin Medical UniversityHarbinChina
  2. 2.Genomics Research Center (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China)Harbin Medical UniversityHarbinChina
  3. 3.School of Public HealthShenzhen University Health Science CenterShenzhenChina

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