Department of Mathematics and Statistics, South Dakota State University, Brookings, SD, USA.
Methods Mol Biol. 2021;2284:417-443. doi: 10.1007/978-1-0716-1307-8_22.
RNA sequencing (RNA-seq) has become a routine method for transcriptomic profiling. We developed a user-friendly web app called iDEP (integrated differential expression and pathway analysis) to help biologists interpret read counts or other types of expression matrices derived from read mapping. With iDEP, users can easily conduct exploratory data analysis, identify differentially expressed genes, and perform pathway analysis. Due to its intuitive user interface and massive annotation database, iDEP is being widely adopted for interactive analysis of RNA-seq data. Using a public dataset on the effect of heat shock on mouse with and without functional Hsf1, we demonstrate how users can prepare data files and conduct in-depth analysis. We also discuss the importance of critical interpretion of results (avoid p-hacking and rationalizing) and validation of significant pathways by using different methods and independent annotation databases.
RNA 测序（RNA-seq）已成为转录组分析的常规方法。我们开发了一个名为 iDEP（综合差异表达和通路分析）的用户友好型网络应用程序，帮助生物学家解释从读取映射得出的读取计数或其他类型的表达矩阵。使用 iDEP，用户可以轻松进行探索性数据分析，识别差异表达基因，并进行通路分析。由于其直观的用户界面和庞大的注释数据库，iDEP 被广泛用于 RNA-seq 数据的交互式分析。我们使用一个关于热休克对有功能 Hsf1 和没有功能 Hsf1 的小鼠影响的公共数据集，演示了用户如何准备数据文件并进行深入分析。我们还讨论了通过使用不同的方法和独立的注释数据库对结果进行关键解释（避免 p 值操纵和合理化）和验证显著通路的重要性。
