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Preprint

Gene Set enrichment analysis

HM Hannah R Monday
PC Pablo Castillo

Last updated date: Jan 14, 2026 Views: 22 Forks: 0

original An abbreviated version of this protocol was published in eLife in Sep, 2020
CB1-receptor-mediated inhibitory LTD triggers presynaptic remodeling via protein synthesis and ubiquitination
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Protocol for GSEA/GO

  • Take the mean of forward and reverse experiments.
  • Rank the list and submit to GSEA (Gene set Enrichment Analysis) against Gene-Ontology (GO) database. This software is free to download online and easy to use.
    • Since we pre-ranked list use ‘Run GSEAPreranked’. Requires a list in .rnk format. 
    • This reflects the degree to which a gene set is overrepresented at the top or bottom of a ranked list of genes
    • Control is a permutated dataset (1000 iterations)
  • 40 GO terms passed the threshold
  • Then perform enrichment mapping
    • Take all GO and measure similarity
    • Node size represent enrichment in the data
    • Edges represent similarity between GO terms
Copyright: © 2026 The Author(s); This is an open-access article under the CC BY-NC license (https://creativecommons.org/licenses/by-nc/4.0/).
How to cite：
Readers should cite both the Bio-protocol preprint and the original research article where this protocol was used:
  1. Monday, H and Castillo, P(2026). Gene Set enrichment analysis. Bio-protocol Preprint. bio-protocol.org/prep2891.
  2. Monday, H. R., Bourdenx, M., Jordan, B. A. and Castillo, P. E.(2020). CB1-receptor-mediated inhibitory LTD triggers presynaptic remodeling via protein synthesis and ubiquitination. eLife. DOI: 10.7554/eLife.54812

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