ABSTRACT

RNA-sequencing (RNA-seq) analysis of gene expression and alternative splicing should be routine and robust but is often a bottleneck for biologists because of different and complex analysis programs and reliance on specialized bioinformatics skills. We have developed the ‘3D RNA-seq’ App, an R shiny App and web-based pipeline for the comprehensive analysis of RNA-seq data from any organism. It represents an easy-to-use, flexible and powerful tool for analysis of both gene and transcript-level gene expression to identify differential gene/transcript expression, differential alternative splicing and differential transcript usage (3D) as well as isoform switching from RNA-seq data. 3D RNA-seq integrates state-of-the-art differential expression analysis tools and adopts best practice for RNA-seq analysis. The program is designed to be run by biologists with minimal bioinformatics experience (or by bioinformaticians) allowing lab scientists to analyse their RNA-seq data. It achieves this by operating through a user-friendly graphical interface which automates the data flow through the programs in the pipeline. The comprehensive analysis performed by 3D RNA-seq is extremely rapid and accurate, can handle complex experimental designs, allows user setting of statistical parameters, visualizes the results through graphics and tables, and generates publication quality figures such as heat-maps, expression profiles and GO enrichment plots. The utility of 3D RNA-seq is illustrated by analysis of data from a time-series of cold-treated Arabidopsis plants and from dexamethasone-treated male and female mouse cortex and hypothalamus data identifying dexamethasone-induced sex- and brain region-specific differential gene expression and alternative splicing.

摘要

基因表达和选择性剪接的 RNA 测序 (RNA-seq) 分析应该是常规且可靠的，但由于不同且复杂的分析程序以及对专业生物信息学技能的依赖，这往往成为生物学家的瓶颈。我们开发了“3D RNA-seq”应用程序，这是一款 R 闪亮应用程序和基于网络的管道，用于全面分析任何生物体的 RNA-seq 数据。它代表了一种易于使用、灵活且强大的工具，用于分析基因和转录本水平的基因表达，以识别差异基因/转录本表达、差异选择性剪接和差异转录本使用 (3D) 以及从 RNA 到同种型的转换。序列数据。3D RNA-seq 集成了最先进的差异表达分析工具，并采用 RNA-seq 分析的最佳实践。该程序旨在由具有最少生物信息学经验的生物学家（或生物信息学家）运行，允许实验室科学家分析他们的 RNA-seq 数据。它通过用户友好的图形界面进行操作来实现这一点，该界面可自动执行管道中程序的数据流。3D RNA-seq 执行的综合分析极其快速和准确，可以处理复杂的实验设计，允许用户设置统计参数，通过图形和表格可视化结果，并生成出版质量数据，例如热图、表达谱和GO 富集图。通过分析冷处理拟南芥植物的时间序列数据以及地塞米松处理的雄性和雌性小鼠皮层和下丘脑数据，识别地塞米松诱导的性别和大脑区域特异性差异基因，说明了 3D RNA-seq 的实用性表达和选择性剪接。