Question: Interpreting DEseq2 results
0
gravatar for roy.granit
5 months ago by
roy.granit800
Israel/LabWorm
roy.granit800 wrote:

I ran an mRNA seq analysis with three groups: control, treated1, treated2 - each with two replicates.

When I look at the comparison of 'treated2 vs control' I notice that most of the genes that hit statistical adjusted p-value are 'log2FoldChange' positive - meaning they are up-regulated in treated2.

Does this make sense? I guess I would expect to see relative equal numbers of up/down regulated genes.. what can you make of this?

Thanks

deseq2 • 252 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by roy.granit800
2

That sounds like more of a biology question than a bioinformatics question. Based on the treatment would you expect global/general upregulation? Some treatments cause global gene silencing/upregulation so those results would be expected.

Are you also applying a log2FoldChange cutoff? If you apply that cutoff (look for genes with |log2FC| > 1 and FDR < 0.05) do you still see this pattern?

ADD REPLYlink written 5 months ago by shawn.w.foley780

To add to the above, it would also be useful to know if you are applying a minimum count cutoff per gene? Perhaps if you are applying a cutoff well above the default, it could be removing a certain number of genes (up and down-regulated), although of course removing low-expressing genes also has an effect on FDR adjustment. Just a few more details would be helpful.

ADD REPLYlink written 5 months ago by lshepard340

roy.granit, the point by lshepard is quite valid. Indeed, nobody can really answer your question because you have not given a great amount of detail about your entire processing pipeline. It is also important to know how you derived the raw counts that you input to DESeq2.

ADD REPLYlink written 5 months ago by Kevin Blighe45k

Thanks everyone. I'm not applying any cutoffs other than FDR < 0.05.

As for the details, this is 3' RNAseq lib which I have aligned to the genome/transcriptome using STAR and counted the reads with Salmon.

My main concern was that this is caused by some mistake in the analysis pram, but since in this case I believe that can provide a reasonable biological explanation.

ADD REPLYlink written 5 months ago by roy.granit800

Okay, cool.

ADD REPLYlink written 5 months ago by Kevin Blighe45k

How does the MA plot look like?

ADD REPLYlink modified 5 months ago • written 5 months ago by Asaf6.1k

Looks pretty equal..

ADD REPLYlink written 5 months ago by roy.granit800
1

Then you should be fine. Many times you only get genes up or down regulated

ADD REPLYlink written 5 months ago by Asaf6.1k
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