Interpreting this plot from GSEA I have RNA-seq for two groups of patients: Responders to chemotherapy (n=9) versus non-responders to chemotherapy (n=24)
I have done DESeq2 and obtain fold change of responders versus non-responders in which positive fold change means down-regulation in responders (if I am not wrong)
&gt; head(df)
    gene       FC
1 286499 7.116071
2 260436 6.691189
3   2267 5.751322
4   5968 5.522079
5   4103 5.328008
6 442709 5.036087
&gt; 

I have done GSEA in pre-ranked way
got this plot for KRAS pathway

I interpret this as; KRAS pathway in being down regulated in responders
Am I right?
Please correct me
When I separated genes for up and down regulated
For up regulated genes I did not get any significant GSEA but for down regulated genes in responders I got this

SO does this mean that KRAS pathway is being up regulated in responders because I have used down regulated genes in responders?
In Deseq2, it depends on contrast eg. if your contrast &lt;- c(&quot;Condition&quot;, firstC, SecondC) is then -ve is downregulated in FirstC and same for +ve. It is always better to take look at count data for the confirmation (responders versus non-responders samples).
[for more detail you can refer here][1]
[1]https://github.com/amarinderthind/RNA-seq-tutorial-for-gene-differential-expression-analysis/blob/master/RNA-Seq-DGE.R