Hi friends,
I am doing GSEA for specific pathways. I want to analyze my genes with the gene sets in specific pathways, such as the metabolism of carbohydrates, lipids, proteins, etc. I am using the REACTOME database as a source. I also want databases of other pathways like inflammation, energy metabolism, and so on (these are not available in REACTOME). What other databases are available and also commonly used for GSEA?
Would be helpful in you could give me some ideas. Thanks
2 answers
You don't mention what organism your are working with, but MSigDB may be a suitable option for you - you can manually download many different formats of individual gene sets or gmt files of whole collections e.g., https://www.gsea-msigdb.org/gsea/msigdb/human/collections.jsp#H
REACTOME contains those already, but you have to put some biological knowledge. Inflammation itself is not a pathway, but you can go for cytokine signaling, Interleukin-1 cascade, inflammasomes, apoptosis, leukocyte recruiment, so the actual components of an inflammatory process. Same goes for energy metabolism, you can go for glycolysis, beta-oxidation, pentose pathway, things like that. Usually these terms are a bit more refined compared to these very broad names you mention.
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Some commonly used databases for GSEA other than Reactome include KEGG, Biocarta, WikiPathways, GO, and more. If you are using the GSEA IDE then an extensive list of gene sets databases can be seen from the drop down menu on the "Run GSEA" tab located on the left side. In my opinion the IDE is very useful for performing GSEA for the first time to quickly see the effects of changing different parameters (e.g.,permutation type).
Thank you @FrankStarling
I viewed the databases you mentioned. But how can I download gene sets related to the pathways from these sites?
I want files as gmt or excel formats.
KEGG is not fully open as it requires a subscription, so you will not get lists straight away. I would generally stick to REACTOME as it is at least fully open.source and with citations where these terms come from. KEGG is (for me) a blackbox.