Gene set enrichment analysis
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aogunbaw • 0
@17490ccc
Last seen 14 days ago
United States

Hello,

I am trying to do a geneset enrichment analysis using gseGO in Clusterprofiler. However, I only have the entrez gene ID and gene name.

Is it possible to run a gene set enrichment analysis with just the gene ID information without having a log2FC for my geneList?


# what the code is supposed to look like for the enrichment 
#However I only have the geneID information, for the geneList and this wouldn't run.

ego3 <- gseGO(geneList = geneList, OrgDb = org.Hs.eg.db, ont = "CC", minGSSize = 100, maxGSSize = 500, pvalueCutoff = 0.05, verbose = FALSE) ```

clusterProfiler GeneSetEnrichment • 209 views
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Guido Hooiveld ★ 4.0k
@guido-hooiveld-2020
Last seen 2 days ago
Wageningen University, Wageningen, the …

No, that is not possible. The idea of gene set enrichment analysis (GSEA) is that it checks which gene sets (pathways, GO categories) are enriched at the top, or bottom, of a ranked list of input genes.

I don't know your use case, but if your genes have been selected on e.g. a significance cutoff, then you could consider performing an over-representation analysis (ORA) (hrough the function enrichGO()). See e.g. for more on this here: https://yulab-smu.top/biomedical-knowledge-mining-book/enrichment-overview.html (section 5.2 and 5.3).

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