GSEA Plot interpretation

[Sebastian FANTINI]

Hi everyone,

I am currently trying to analyze RNA-seq data with GSEA.

just to make sure you have interpreted the results correctly, I report some curves and related interpretations:

A) (taken from GSEA website): the geneset of interested is enriched in gene up-regulated in the ranked gene list (so up-regulated in the first phenotype, let say the "numerator"). However I cannot strictly conclude that this geneset is activated functionally in the first phenotype. Is it correct?

B) (taken from our results): the geneset of interested is enriched in gene down-regulated in the ranked gene list (so down-regulated in the first phenotype, let say the "numerator", or up-regulated in the second phenotype, the denominator).

Is it possible to conclude something for figures C) and D)?

Is it possible from GSEA analysis to evaluate if a geneset is functionally activated or repressed?

Thank you so much,

Sebastian

[Anthony Castanza]

Hi Sebastian,

GSEA simply reports the coordinated shifts of sets of genes, this can be used to infer activation or repression based on the experiment you performed but isn't strictly speaking in and of itself a direct assay.

Your comparison to the numerator and denominator is correct here and a good understanding of the symmetricality of GSEA results.

I'm hesitant to offer specific interpretations of your results because I don't know anything about the experiment you performed, or the statistics that GSEA returned for those sets but I would not expect the enrichment of the result in D to be particularly meaningful. C is potentially interesting, it appears as if there are components of the set that are regulated in opposite directions. If this would be an informative result for you, I might suggest taking the set and putting it into GSEA's overlap statistic tool to see if you can find more sets in MSigDB that are encompassing those genes and see if you can tease apart those two components.

Hope this helps

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

--
You received this message because you are subscribed to the Google Groups "gsea-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to gsea-help+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/2f4af02b-3016-4a90-b50f-4cf8afdfd69en%40googlegroups.com.

[Sebastian FANTINI]

Hi Anthony,

thank you so much for your kind reply.

Nice to hear that my interpretation was basically correct.

When you suggest to use GSEA's overlap statistic tool, are you referring to the "Compute overlaps tool" (showing collections to investigate for overlap with this gene set)?

Thank you very much once more.

Best,

Sebastian

[Anthony Castanza]

Yes, I misspoke there, I was referring to the website's compute overlaps tool.

Let me know if you have any other questions!

-Anthony

Anthony S. Castanza, PhD
Curator, Molecular Signatures Database
Mesirov Lab, Department of Medicine
University of California, San Diego

To view this discussion on the web visit https://groups.google.com/d/msgid/gsea-help/69e421ae-8ce4-4ddf-97e8-113954904e96n%40googlegroups.com.