环状 RNA 表达数据的计算分析。

Computational Analysis of circRNA Expression Data.

机构信息

Department of Computer Science, University of Turin, Turin, Italy.

Department of Clinical and Biological Sciences, University of Turin, Orbassano, Italy.

出版信息

Methods Mol Biol. 2021;2284:181-192. doi: 10.1007/978-1-0716-1307-8_10.

DOI:10.1007/978-1-0716-1307-8_10

PMID:33835443

Abstract

Analysis of circular RNA (circRNA) expression from RNA-Seq data can be performed with different algorithms and analysis pipelines, tools allowing the extraction of heterogeneous information on the expression of this novel class of RNAs. Computational pipelines were developed to facilitate the analysis of circRNA expression by leveraging different public tools in easy-to-use pipelines. This chapter describes the complete workflow for a computationally reproducible analysis of circRNA expression starting for a public RNA-Seq experiment. The main steps of circRNA prediction, annotation, classification, sequence reconstruction, quantification, and differential expression are illustrated.

摘要

从 RNA-Seq 数据中分析环状 RNA (circRNA) 的表达可以使用不同的算法和分析流程来完成，这些工具允许提取关于这种新型 RNA 表达的异质信息。计算流程被开发出来，以便通过在易于使用的流程中利用不同的公共工具，方便 circRNA 表达的分析。本章描述了从公共 RNA-Seq 实验开始，对 circRNA 表达进行可重复计算分析的完整工作流程。说明了 circRNA 预测、注释、分类、序列重建、定量和差异表达的主要步骤。