Need help in GSEA analysis and interpretation

Question

[vinayjrao]

Hello,

I am performing GSEA to study the enrichment of a particular geneset upon tumor induction. I have run the analysis using default parameters and the barcode plot generated only shows 10 significant genes enriched out of 215.

I want to know if it could imply biological significance, or have I made a mistake in the analysis?

Thank you.

Edit:

I'm sorry for the incomplete information, I used the GSEA tool published by Broad Institute. The organism was human, and I was specifically looking into the HR Defect signature as described by Peng et al. The aim is study the enrichment of the geneset after tumor induction.

Answer 1

[caggtaagtat]

You mean 10 geneSETS ?

It's hard to guess biological significance with this little information. However, 10 sounds quiet little for after tumor induction.

Which tool did you use? What organism are we talking about and which type of genesets did you look at?

[vinayjrao]

It's actually only 10 genes represented in the barcode plot, but yes they belong to 10 different genesets.

I'm sorry for the incomplete information, I used the GSEA tool published by Broad Institute. The organism was human, and I was specifically looking into the HR Defect signature as described by Peng et al. The aim is study the enrichment of the geneset after tumor induction.

Answer 2

[predeus]

What do you mean by "significant genes"? Are they significant in differential expression analysis?

Because GSEA does not generate significant genes, GSEA gives you leading edge genes, and that's different.

Overall, you need to specify 1) what GSEA tool and method have you used; 2) what was the reference GMT file and how many pathways it contained; 3) how many of these pathways were found to be significant.

[vinayjrao]

I'm sorry for the incomplete information, I used the GSEA tool published by Broad Institute. The organism was human, and I was specifically looking into the HR Defect signature as described by Peng et al. The aim is study the enrichment of the geneset after tumor induction.

I used the h.all reference

If GSEA does not give the significant genes, then what do the genes apart from the leading edge subset represent? And when I mentioned significant, I meant these were the genes to show up in the barcode plot, which are a subset of the geneset.