Entering edit mode
4.5 years ago
young_bioinformatician
▴
230
Hi,
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 !
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: http://software.broadinstitute.org/gsea/index.jsp
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 : https://amp.pharm.mssm.edu/Enrichr/.
This works for a number of species and should give you a very good broad look of the processes active in your cells.
Hi V, I have checked it but unfortunately, I use R script that's why it is not really appropriate for me. Thanks !
Hey, there is actually an enrichR package: https://cran.r-project.org/web/packages/enrichR/index.html
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.
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.