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Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2
Published on: September 18, 2021
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bestDEG: a web-based application automatically combines various tools to precisely predict differentially expressed
Unitsa Sangket1,2, Prasert Yodsawat1, Jiratchaya Nuanpirom1
1Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand.
Peerj
|November 17, 2022
Summary
bestDEG is a new web tool that simplifies differential gene expression analysis using RNA sequencing. It combines multiple methods to improve accuracy and provides user-friendly results, reducing the need for complex programming skills.
Area of Science:
- Transcriptomics
- Bioinformatics
- Computational Biology
Background:
- RNA sequencing (RNA-Seq) is a key technique for transcriptome research.
- Existing differential gene expression analysis (DEG) methods have limitations, with no single method outperforming others.
- Combining multiple DEG analysis methods can enhance result validity.
Purpose of the Study:
- To develop a user-friendly web application, bestDEG, for automated differential gene expression analysis.
- To integrate and compare results from multiple DEG analysis tools.
- To provide a consensus method for improved DEG identification.
Main Methods:
- Developed the bestDEG web application.
- Created a differential expression analysis pipeline combining edgeR, DESeq2, NOISeq, and EBSeq packages.
- Evaluated bestDEG using human datasets from the MicroArray Quality Control (MAQC) project.
Main Results:
- bestDEG demonstrated excellent performance on human datasets.
- The consensus method achieved high precision (94.71%) and specificity (97.01%).
- bestDEG offers a user-friendly interface, Venn diagrams, and result tables.
Conclusions:
- bestDEG is an efficient tool for analyzing differentially expressed genes (DEGs).
- The consensus method maximizes precision and minimizes false discovery rates, reducing experimental costs.
- bestDEG empowers users without programming knowledge to perform complex DEG analysis.
