GSEA documentation

Question

[Eliza]

Hi, I was wondering if there is a detailed documentation on what is GSEA and how it works .

Thanks

[GenoMax]

You may have already seen:

https://www.gsea-msigdb.org/gsea/doc/GSEAUserGuideFrame.html
https://docs.gsea-msigdb.org/#GSEA/GSEA_User_Guide/

Answer 1

[biofalconch]

Ming Tommy Tang just published a tutorial on how to do it and what it is :)

How to do GSEA in R for RNAseq data

[Eliza]

biofalconch thank you , is there perhaps a paper expalining exactlywhat is GSEA and how GSEA works ? In context to my reaserch i have genes from my experiment and another predefined gene set associated with a skin disease I whish to examine if the genes from my expirement are enriched with the gene set from the skin disease , is GSEA the correct tool for that ?

[biofalconch]

Perhaps this paper could help :) I think it could be helpful in your case, it will definitely show wether the set is also upregulated on other conditions :)

Gene set enrichment analysis: A knowledge-basedapproach for interpreting genome-wideexpression profiles

[Eliza]

biofalconch, thank you :) also, I was wondering if there is a recommended R package that preforms GSEA in which I can input my expreriment gene data and the pre defined gene set also if there is an option to use this without gene expression information ? . the L and S here:

[biofalconch]

I guess most people use clusterProfiler, in the tutorial I mention above Tommy teaches how to use it :), also the documentation is ok to walk you through it

[Ming Tommy Tang]

Thanks, biofalconch :) I wrote a post to explain it too https://crazyhottommy.blogspot.com/2016/08/gene-set-enrichment-analysis-gsea.html