isoTar: Consensus Target Prediction with Enrichment Analysis for MicroRNAs Harboring Editing Sites and Other Variations.

• 发表时间: 2019
• 来源期刊: Methods Mol Biol
• DOI: 10.1007/978-1-4939-9207-2_12
• PMID: 30963495
• 文章类型: Journal Article
• 作者列表: Distefano R,Nigita G,Veneziano D,Romano G,Croce CM,Acunzo M

关键词: A-to-I RNA editing; ADAR; Editome; IsomiRs

Mesh: Computational Biology / methods; Consensus; Gene Expression Regulation; Genetic Variation; High-Throughput Nucleotide Sequencing; Humans; MicroRNAs / genetics metabolism; RNA Editing; RNA, Messenger / genetics metabolism; Sequence Analysis, RNA; Software

Abstract

MicroRNAs (miRNAs) are small noncoding RNA molecules (sncRNAs) involved in gene expression regulation. Having been widely studied during last two decades, they have been associated with several diseases, including cancer. Recent improvements in high throughput sequencing technologies have revealed a more complex miRNAome, due to miRNA sequence modification phenomena, such as RNA editing and isomiRs. As a result, a new class of tools is necessary in order to appropriately investigate this emerging complexity. To address such need, we developed isoTar, a high-performance Web-based containerized application designed for miRNA consensus targeting prediction and functional enrichment analyses. In the present chapter, we provide an overview of isoTar ( https://ncrnaome.osumc.edu/isotar/ ), as well as benchmarks and a guide to its usage.