Question: Interpreting Differentially Expressed Genes(DEGs) from RNA Seq experiment
0
gravatar for benjyrolls
19 months ago by
benjyrolls70
benjyrolls70 wrote:

I have a list of Differentially Expressed Genes(DEGs) from an experiment which involved a mouse model with Sox2 and another model with Sox2 Knock Out( Sox2 WT vs Sox2 KO).

What conclusions can I make from these DEGs and what can I say of these genes in terms of Sox2 ?

thanks

Benjy

rna-seq • 1.0k views
ADD COMMENTlink modified 19 months ago by igor7.1k • written 19 months ago by benjyrolls70
2

What was the biological question for which this project was started?

ADD REPLYlink written 19 months ago by WouterDeCoster35k
1

I don't think anyone can answer this question without knowing what are the genes affected by Sox2 KO. Anyway, have you tried looking if specific classes of genes are affected ? Perhaps this could help you interpreting your results.

ADD REPLYlink written 19 months ago by Carlo Yague4.3k
2
gravatar for Devon Ryan
19 months ago by
Devon Ryan86k
Freiburg, Germany
Devon Ryan86k wrote:

You can conclude that, at least in the context of the tissue/environment of the mouse strain you're using, that Sox2 KO affects their expression. If there's a Sox2 binding site (see ChIPseq data) in the promoter then this is likely a direct effect. Otherwise it may be indirect.

ADD COMMENTlink written 19 months ago by Devon Ryan86k
1
gravatar for igor
19 months ago by
igor7.1k
United States
igor7.1k wrote:

If you have trouble interpreting results based on individual genes, you can do gene sets or pathways analysis. That will tell you if your differentially expressed genes are linked to a specific biological process.

ADD COMMENTlink written 19 months ago by igor7.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1674 users visited in the last hour