Question: Interpreting Differentially Expressed Genes(DEGs) from RNA Seq experiment
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gravatar for benjyrolls
2.4 years 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 • 1.4k views
ADD COMMENTlink modified 2.4 years ago by igor8.6k • written 2.4 years ago by benjyrolls70
2

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

ADD REPLYlink written 2.4 years ago by WouterDeCoster41k
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 2.4 years ago by Carlo Yague4.7k
2
gravatar for Devon Ryan
2.4 years ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k 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 2.4 years ago by Devon Ryan92k
1
gravatar for igor
2.4 years ago by
igor8.6k
United States
igor8.6k 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 2.4 years ago by igor8.6k
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