What Are DEGs? Differentially Expressed Genes in RNA-Seq
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What Are DEGs?
DEGs stands for Differentially Expressed Genes -- genes whose expression levels are significantly upregulated or downregulated between conditions or groups.
What Is Differential Expression Analysis?
Differential expression analysis is the process of identifying DEGs. It is commonly performed after genome-wide gene expression profiling such as RNA-Seq or microarray experiments.
For example, an RNA-Seq experiment in humans yields expression data for tens of thousands of genes, making it difficult to interpret the results as-is. (The expression table below shows only nine genes for illustration, but a real experiment produces data for tens of thousands.)
Example of an Expression Table
By extracting genes that are significantly upregulated or downregulated from among these tens of thousands of genes, biological interpretation becomes much more tractable. The result is a smaller set of differentially expressed genes, as shown below.
Example of DEG Analysis Results
A variety of software tools have been developed for differential expression analysis. Popular options include edgeR, DESeq2, and Ballgown.
Functional Analysis After DEG Identification
Differential expression analysis produces a gene list. When the list is short, you can examine each gene individually. However, when it contains many genes, interpretation becomes difficult.
For this reason, functional analysis is often performed after DEG identification. Functional analysis identifies which biological functions are overrepresented among the genes in the list.
The most common frameworks for functional analysis are Gene Ontology (GO) and biological pathways. These are referred to as GO analysis and pathway analysis, respectively.
See the pages below for more details on GO analysis and pathway analysis.
Example of Gene Ontology Analysis
Example of Pathway Analysis
RNA-Seq Data Analysis Software
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Users can perform gene expression quantification, identification of differentially expressed genes, gene ontology(GO) analysis, pathway analysis, as well as drawing volcano plots, MA plots, and heatmaps.
About the Author
BxINFO LLC
A research support company specializing in bioinformatics.
We provide tools and information to support life science research, with a focus on RNA-Seq analysis.