Microarray-Based MicroRNA Expression Data Analysis with Bioconductor.

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.