how to run GSEA analysis on the custom genesets (example is provided)

[Dong]

Hello, 

I have gene expression data of both human and mouse tumor samples from both microarray and RNAseq analysis.  I want to look at different types of immune cells in the samples.  Below is the link for the paper providing the example. See Fig. 2, panel B and E.  In the supplementary table 6, a list of 782 immune-related genes is provided.  My guess is that they ran their gene list against this custom genesets using GSEA.  But I don't know how to do that.  I hope that I can get some help on this which will be important for my project.  

https://www.sciencedirect.com/science/article/pii/S2211124716317090?via%3Dihub#app2 

Thanks.

Dong

[Anthony Castanza]

Hi Dong,

 

You can create custom gene set database files according to the specifications here:

https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#Gene_Set_Database_Formats

 

for just one set you might want to use the GRP format, it is the simplest one. Also, the set you've described is above the normal default maximum size, so you you'll want to increase Max Size exclude larger sets to something >782

 

Finally, you might want to remap the symbols in your gene set to the latest versions in MSigDB, there isn't a super convenient way to do that but it can be done with MSigDB's Symbol remapping CHIP files, or if you run the list in MSigDB's Investigate Gene Sets webtool, where on the results page it says " click here for details" you can copy and paste that table into excel and extract the Gene Symbol column.

 

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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[Dong]

Hi Anthony, 

I notice that figure 2a mentioned about ssGSEA.  What is the really difference between ssGSEA and GSEA?

Thanks.

Dong