Interpreting GSEA enrichment plots/results

Question

[vinayjrao]

Hi,

To address a particular question, concerning a particular gene, which we hypothesize is involved in reducing DNA damage repair, we decided to analyze RNA-Seq data from TCGA. Upon analysis, we found that the particular gene is overexpressed in breast cancer, but we could not get an enrichment in HR deficient signature (a set of genes, which when enriched lead to a repression of Homologous Recombination) using GSEA.

We then set out to check for enriched (KEGG) pathways again using GSEA, and also checked for positional gene sets enrichment, which gave me the following enrichment plots -

for KEGG pathway enrichment, and

for positional gene sets enrichment.

Could you please guide me in the interpretation of these data? I also have the relevant .html files for each of the plots shown below, if anyone needs them to explain this to me.

Thanks in advance :)

Answer 1

[restonpiston]

I was in your position a few weeks ago, and I found this link from GSEA in the generated report.

The peak point of the green plot is your ES (enrichment score), which tells you how over or under expressed is your gene respect to the ranked list.

The second part of the graph (middle with red and blue) shows where the rest of genes related to the pathway or feature are located in the ranking.

The third part of the grapth (bottom with gray part) shows how your metric is distributed along the list.

What would you like to know about this data?