How to perform a GSEA and visualize it the best way

Question

[frida.danielsson]

Hi,

If you have a list of genes (about 200 that localize to a common organelle) and you would like to know what type of functions that are enriched among these, what tools would you use and how could the results from such an analysis best be visualized?

/Frida

Answer 1

[Nathaniel]

It depends on the kind of gene ontology enrichment analysis that you want to do. If you have two conditions together with the expression levels in each condition, then you can use GSEA itself (read the paper to make sure it is what you want to do), which you can find here: http://software.broadinstitute.org/gsea/index.jsp). If you only consider the gene names, then take a look at Gorilla http://cbl-gorilla.cs.technion.ac.il/

[frida.danielsson]

Thanks a lot, I have no other info than just the gene names, I will try gorilla then!

Answer 2

[WouterDeCoster]

Gene enrichment testing can also be performed using these excellent sites:

Enrich: http://amp.pharm.mssm.edu/Enrichr/

Webgestalt: http://bioinfo.vanderbilt.edu/webgestalt/login.php