GSEA data interperetation

[Mai Nguyen]

Dear Mr/Ms,

I am a person who is new person in GSEA analysis. I try to analyze GSEA with ranked list genes and get data. However, I don't know how to read and interpret data to determine which gene set is significant. 

example this is my data which I got from GSEA analysis: 

And how can I choose data to get leading edge analysis and how can I set parameter for enrichment map visualization? 
i am sorry that I ask a lot of question and information related to GSEA analysis. But can you help me to answer this question? Thank you so much. 

Sincerely yours, 
Mai Nguyen

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Ms. Mai Nguyen
Tel: 82 10 2482 1985
Email: tienp...@gmail.com

[Anthony Castanza]

Hello Mai,

I would encourage you to first examine the user guide we offer, particularly the section on interpreting GSEA results: https://docs.gsea-msigdb.org/#GSEA/GSEA_User_Guide/#interpreting-gsea-results

This user guide gives guidance on appropriate significance thresholds (generally NOM pValue < 0.05, FDR <0.25 if using phenotype permutation mode, or <0.05 in gene set permutation mode).

The leading edge analysis tool within GSEA is also documented within our user guide:https://docs.gsea-msigdb.org/#GSEA/GSEA_User_Guide/#running-a-leading-edge-analysis

For use of Enrichment Map, which is developed and maintained by the Bader Lab, I would refer you to Enrichment Map's Documentation: https://baderlab.org/Software/EnrichmentMap

These things aside, I noticed that the enrichment plots for your data, particularly the ranking metric plot component don't quite look right. It would appear that the data you submitted to GSEA only has ~200 genes. This is not the correct way to run this analysis. GSEA should be provided the full dataset of all expressed genes, and not just those that, for example, pass significance thresholds. I would encourage you to re-run this analysis with the complete dataset.

Please let me know if you have any additional questions after reviewing the GSEA documentation.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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