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Interpreting Differentially Expressed Genes(DEGs) from RNA Seq experiment

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
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updated by igor igor • written by benjyrolls benjyrolls

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.

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written by Carlo Yague Carlo Yague

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

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written by WouterDeCoster WouterDeCoster

2 answers

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.

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written by Devon Ryan Devon Ryan

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.

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written by igor igor

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