Following up on Hallmark50 hits

[ilian atanassov]

Dear Devs,

The Molecular Signatures Database (MSigDB) is a popular resource for gene sets. Their refined "hallmark" gene sets, 50 so far, that are derived from multiple "founder" sets, https://www.sciencedirect.com/science/article/pii/S2405471215002185?via%3Dihub . The hallmark sets provide a summary of the founder sets, and can be very useful for high biological level gene set enrichment analysis. Webgestalt supports the use of the hallmark gene sets, "Functional Database" -> "community-contribured" -> "Hallmark50",   and "Gene/Hallmarks" example.

One of the recommendations for using the Hallmark gene set is the following, "In order to, take full advantage of hallmarks and the exploratory nature of GSEA, we recommend proceeding through a series of GSEA analysis stages (see box 1)". Box 1 is attached below which follows the simple workflow of 1) perform GSEA using hallmark 50 2) identify significant hallmark gene sets 3) repeat GSEA using the founder set for the respective significant hallmark gene sets and then 4) complement the results using other, function-specific, MSigDB gene sets.

I would like to ask about the "best" way to execute this strategy in WebGestalt and whether you have plans to include the groups of founder gene sets, which correspond to specific hallmark gene sets, in addition to the already available Hallmark50 / community-contributed_Hallmark50.

Best wishes,
Ilian