Hello all,
I am having trouble finding information about the gene set enrichment pathways (columns) in ssGSEA_Public_24Q2_subsetted. For example, I would like to know which genes are included in each pathway or a brief description of the pathway itself.
I tried searching for each pathway on GSEA | MSigDB | Browse Human Gene Sets but even if I search key words of a pathway there are no results.
The gene sets are from MSigDB so I’m surprised that you’re not finding the definitions there. Can you provide the name of a pathway which is not present in MSigDB?
I picked an arbitrary column name (BIOCARTA_KREB_PATHWAY) and searched on MSigDB and it came up with a match:
Are you seeing something different, or am I misunderstanding your question?
Thanks,
Phil
Hi Phil,
Thank you for your response.
When I search a column that does not begin with GO_ I am able to get a result. However, if I try searching a GO_(pathway) no results are found even if I search just a key word. Below is a search for GO_L_METHIONINE_SALVAGE_FROM_METHYLTHIOADENOSINE.
The issue appears to be due to our using a very old version of MSigDB for these gene sets. Specifically, it appears we were using v7.2 which you can download from MSigDB’s archive.
If you download that release, I believe you’ll find the gene sets that match the column names in the GSEA dataset.
(I say “were” because we’ve stopped updating the GSEA dataset in the portal and it will stay frozen at the version derived from data from the 24Q2 release.)
Thanks,
Phil
