相关实验视频

Updated: Jun 19, 2025

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2

Published on: September 18, 2021

评估RNA-Seq工作流程方法使用香农透

Nicolas Carels¹

¹Laboratory of Biological System Modeling, Center of Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro 21040-900, RJ, Brazil.

|July 26, 2024

概括

本研究确定了最佳的RNA-sequencing (RNA-seq) 工作流程,以保存生物数据. 将TPM,RLE和TMM正常化与log2折变化的结合最好地保留RNA-seq分析中的生物事实.

科学领域:

生物信息学是一种生物信息学.
基因组学就是基因组学.
计算生物学计算生物学

背景情况:

RNA测序 (RNA-seq) 数据处理缺乏标准化的工作流程,阻碍了可靠的生物解释.
现有的方法在准确捕获RNA-seq数据中的生物信号的能力方面有所不同.

研究的目的:

评估和确定最有效的RNA-seq工作流程来保存生物事实.
评估香农作为优化RNA-seq分析管道的度量.

主要方法:

香农被用来测量RNA-seq数据的生物状态.
分析了多种RNA-seq工作流程方法,包括DESeq2和edgeR.
在TCGARNA-seq数据集上测试了9种与log2倍变化结合的正常化方法,来自12种癌症类型的515名患者.

主要成果:

当用于差异基因表达的log2折变化值≥1时,TPM,RLE和TMM规范化方法表现出优异的性能.
这些最佳组合有效地保留了RNA-seq数据集中的生物信息.

结论:

农提供了评估和优化RNA-seq工作流程的客观度量.
确定的工作流 (TPM,RLE或TMM正常化与log2折变化≥1) 提高了RNA-seq数据分析和mRNA测序技术的准确性.

关键词:

五年制的操作系统.个人个人信息网络PPI网络.在 RPKMM 中.基准测试 (benchmarking) 是一种比较的方法.癌症癌症癌症癌症癌症进入的过程中,中位数的正常化.

更多相关视频

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

RNA Secondary Structure Prediction Using High-throughput SHAPE

RNA Secondary Structure Prediction Using High-throughput SHAPE

Published on: May 31, 2013

相关概念视频

RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

Ribosome Profiling

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...