Question: The meaning of differentially expressed (DE) gene level
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gravatar for Grunir112
4.2 years ago by
Grunir11210
Grunir11210 wrote:

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.

rna-seq sequence gene • 2.3k views
ADD COMMENTlink modified 4.2 years ago by sysbiocoder180 • written 4.2 years ago by Grunir11210
3
gravatar for Devon Ryan
4.2 years ago by
Devon Ryan98k
Freiburg, Germany
Devon Ryan98k wrote:
  • "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).

ADD COMMENTlink written 4.2 years ago by Devon Ryan98k

Thank you for the answer!

ADD REPLYlink written 4.2 years ago by Grunir11210

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

ADD REPLYlink written 11 days ago by Wox440
1

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.

ADD REPLYlink written 9 days ago by Devon Ryan98k
1
gravatar for sysbiocoder
4.2 years ago by
sysbiocoder180
sysbiocoder180 wrote:

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.

ADD COMMENTlink written 4.2 years ago by sysbiocoder180
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