Deep sequencing reveals a microRNA expression signature in triple-negative breast cancer
Journal
Methods in Molecular Biology
Journal Volume
1699
Pages
99-111
Date Issued
2018
Author(s)
Abstract
Deep sequencing is an advanced technology in genomic biology to detect the precise order of nucleotides in a strand of DNA/RNA molecule. The analysis of deep sequencing data also requires sophisticated knowledge in both computational software and bioinformatics. In this chapter, the procedures of deep sequencing analysis of microRNA (miRNA) transcriptome in triple-negative breast cancer and adjacent normal tissue are described in detail. As miRNAs are critical regulators of gene expression and many of them were previously reported to be associated with the malignant progression of human cancer, the analytical method that accurately identifies deregulated miRNAs in a specific type of cancer is thus important for the understanding of its tumor behavior. We obtained raw sequence reads of miRNA expression from 24 triple-negative breast cancers and 14 adjacent normal tissues using deep sequencing technology in this work. Expression data of miRNA reads were normalized with the quantile-quantile scaling method and were analyzed statistically. A miRNA expression signature composed of 25 differentially expressed miRNAs showed to be an effective classifier between triple-negative breast cancers and adjacent normal tissues in a hierarchical clustering analysis. ? 2018, Springer Science+Business Media LLC.
SDGs
Other Subjects
microRNA; microRNA 126 3p; microRNA 1301; microRNA 130b 3p; microRNA 139 5p; microRNA 143 5p; microRNA 145 5p; microRNA 183 5p; microRNA 19b 3p; microRNA 204 5p; microRNA 215; microRNA 24 2 3p; microRNA 320a 5p; microRNA 335 3p; microRNA 362 3p; microRNA 362 5p; microRNA 429 5p; microRNA 489 5p; microRNA 497 5p; microRNA 96 5p; microRNA let 7a 3p; ribosome RNA; transcriptome; transfer RNA; unclassified drug; microRNA; transcriptome; adult; aged; clinical article; controlled study; gene expression; gene regulatory network; human; human genome; human tissue; immunohistochemistry; middle aged; RNA analysis; RNA sequence; sequence alignment; triple negative breast cancer; very elderly; cluster analysis; female; gene expression profiling; gene expression regulation; genetics; high throughput sequencing; procedures; sequence analysis; software; triple negative breast cancer; Adult; Cluster Analysis; Female; Gene Expression Profiling; Gene Expression Regulation, Neoplastic; High-Throughput Nucleotide Sequencing; Humans; MicroRNAs; Sequence Analysis, RNA; Software; Transcriptome; Triple Negative Breast Neoplasms
Publisher
Humana Press Inc.
Type
book part