Interpreting Differentially Expressed Genes(DEGs) from RNA Seq experiment

Question

[benjyrolls]

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

[WouterDeCoster]

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

[Carlo Yague]

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.

Answer 1

[Devon Ryan]

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.

Answer 2

[igor]

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.