Sep 29, 2025

Public workspaceGSEA

DOI
https://dx.doi.org/10.17504/protocols.io.eq2ly492qlx9/v1
  • Maria Jose Perez J.1
  • 1Institut Imagine
  • Team Deleidi
Federico Bertoli
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DOI: https://dx.doi.org/10.17504/protocols.io.eq2ly492qlx9/v1
Protocol Citation: Maria Jose Perez J. 2025. GSEA. protocols.io https://dx.doi.org/10.17504/protocols.io.eq2ly492qlx9/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: September 29, 2025
Last Modified: September 29, 2025
Protocol Integer ID: 228447
Funders Acknowledgements:
ASAP
Grant ID: ASAP-000420
Abstract
GSEA
Troubleshooting
GSEA of senescence-associated pathways was performed with GSEA software (version v4.3.2; https://www.gsea-msigdb.org) using the Molecular Signatures Database (MSigDB, version v6.2, RRID:SCR_016863)
RNA counts from control and CDDO-Me-treated samples were ranked based on the signal-to-noise ratio (SNR), calculated as (µ_treated – µ_control) / (σ_treated + σ_control).
Genes were sorted in descending order according to the SNR.
GSEA was used to calculate the enrichment score (ES), normalized enrichment score (NES), and corresponding false discovery rate (FDR).
Default GSEA settings were applied, with the permutation parameter set to "gene set" because of the small sample size (n < 7).
The gene set size was restricted to 10–500 genes.
Input data included RNA-seq read counts from all three cell types, a sample label mapping file, and senescence-related gene sets.
Gene sets were obtained from MSigDB (senescence, SASP, and cell cycle regulation) and the manually curated SenMayo SASP gene set (Ref. main text 7, 27–30, 90).