How to get/write a .gmt file corresponding to the databases queried by the gseGO() function of clusterProfiler ?

Question

[am835821]

Hi everyone,

Problem: I would like to write a gene matrix transposed file(.gmt) based on the same version of Gene Ontology used by the gseGO() function in the R clusterProfiler package.

Context: I performed a Gene Set Enrichment Analysis on differentially expressed proteins using gseGO(). Now I would like to visualize deregulated biological pathways with the EnrichmentMap plugin of Cytoscape. To do this, I need to provide a .gmt file based on the same database versions queried by gseGO() but I can't seem to find it or write it.

What I've tried:

• getGenesets(org = "hsa", db = "go", onto = "BP", mode = "GO.db") followed by writeGMT() from EnrichmentBrowser but the gene set sizes are different compared to the gseGO() output. I assume the database versions queried are not the same.
• cross data between the 'org.Hs.eg.db' and 'GO.db' objects with select() from AnnotationDbi to try to build the list of gene sets containing each their list of genes.
• download contents on http://geneontology.org/ but the file formats are different OBO/GAF/GPAD/GPI…

I fail gathering the relevant informations and fully understand how all is articulated so I would appreciate any tips/recommandations to move forward. Maybe use another tools ? convert file formats ? work around the the 'org.Hs.eg.db' and 'GO.db' object ?

Thanks for your time and your help.

R/packages versions :

• R version 4.3.1
• clusterProfiler_4.8.1
• EnrichmentBrowser_2.30.1
• Bioconductor version 3.17 (BiocManager 1.30.21)
• GO.db_3.17.0
• org.Hs.eg.db_3.17.0