The meaning of differentially expressed (DE) gene level

Question

[Grunir112]

Can anyone help me to explain in a simple way to a friend (who is not in bioinformatics field) what differentially expressed (DE) gene level is?

I thought that DE means when you are comparing gene expression in two different groups/samples. But here (https://www.ncbi.nlm.nih.gov/books/NBK10061/) it said, that e.g. cells differentiate through differential gene expression.

[natasha.sernova]

See these posts:

Differential gene expression

Differentially gene expressed analyses of two different samples

A: Differential Expression Analysis Theory/Tutorial For The Statistics Layman

In Deep Sequencing Experiments: What Is Differential Expression?

And also this article:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3227109/

and this presentation:

http://www.cs.cmu.edu/~epxing/Class/10810-06/diffExp.pdf

Below is some tool description:

...the DESeq package

https://www.bioconductor.org/packages/devel/bioc/vignettes/DESeq/inst/doc/DESeq.pdf

Answer 1

[Devon Ryan]

• "differential gene expression" means "changes in gene expression"
• "differentially expressed genes" means "genes whose expression levels are statistically different between groups"

Behold the wonderful intersection of scientific jargon with a weird language (English).

[Grunir112]

Thank you for the answer!

[WUSCHEL]

Hi Devon, just curious to know, in DEG, what do you mean by between groups?

If I have a time-course experiment (3-time points) with several genotypes (WT vs 3 different mutants); and my pairwise comparison is mut vs WT at its time point (e.g. 'mut1_0h-WT_0h', mut2_0h-WT_0h', etc), What does mean by the group?

I just saw your answer, after posting my question Why some statistically differently expressed genes are not DEGs? would be great to have your help to understand this

[Devon Ryan]

A "group" is a biologically meaningful collection of samples. So it could be mutant and wild type, possibly at a single time point. It could be two different time points. It's a generic term in English that has absolutely no special meaning in bioinformatics.

Answer 2

[sysbiocoder]

In simple terms, Differential gene expression in change in expression level between groups. For example, the differential gene expression can be determined between mutated and unmutated, at different time intervals, normal and tumor samples , and so on.