Question: Gene Set Enrichment Analysis
gravatar for ugurcabuk
5 weeks ago by
ugurcabuk20 wrote:


I try to apply GSEA on my data. However, I am a bit confused about the process. For example, I have 10000 genes in my gene expression data. As I understood, firstly I should converted the gene names into appropriate gene ID, like gene symbols. Then, I will download gene sets from database, like Msigdb. The last step is to write function of GSEA and run it. However, Which gene sets should I download ? According to what ? Last but not least, do those gene sets present us to signature of up- and down- regulation ?

Thank you very much in advance !

rna-seq gsea R • 146 views
ADD COMMENTlink written 5 weeks ago by ugurcabuk20

What are you hoping to achieve by using GSEA? - this will help to determine the datasets that you need.

Have you checked the main page:

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by Kevin Blighe51k

I would not use GSEA as it is quite unreliable in my opinion. If you want to do a standard gene enrichment analysis. I would select the genes you are interested in, e.g all upregulated genes, and plug them into a tool like enrichr :

This works for a number of species and should give you a very good broad look of the processes active in your cells.

ADD REPLYlink written 4 weeks ago by V170

Hi V, I have checked it but unfortunately, I use R script that's why it is not really appropriate for me. Thanks !

ADD REPLYlink written 4 weeks ago by ugurcabuk20

Hey, there is actually an enrichR package:

It is easy to use and can quickly generate a lot of data for you to analyse. GSEA is cumbersome to use and I do not use it too much, to be honest.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by Kevin Blighe51k

Hi Kevin, thank you for answering. Okay I will try to explain my procedure. Firstly, I had rna-seq data then I got fold change value from the data. Now, I will make gene set enrichment analysis. I am a bit confused in this step. What is the difference between getting gene sets from database and creating own gene sets ? The goal of gene set enrichment analysis is to find out genes which include in pathways and make a cluster them in specific pathway. I mean, at least my goal is that. So, I have found two library, which are singscore, and gsva. So, What is the next step ? I have input now.

ADD REPLYlink written 4 weeks ago by ugurcabuk20
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