Troubleshooting for no significance in GSEA

[Leo]

Hi, 

I am using GSEA for proteomics data. Although there is strong enrichment in cell cycle-related GO terms in gene ontology enrichment analysis (input the up or down-regulated protein names |log2FC| > 1, padj < 0.1), the GSEA did not show the significance in cell cycle-related hallmark gene sets (e.g. HALLMARK_G2M_CHECKPOINT, HALLMARK_MITOTIC_SPINDLE, like following plot). The GSEA was done by inputting the whole protein list (total 9942). The list was ranked by log2FC. May I ask if there is anything I did wrong or any troubleshooting that I could do? 

GSEA results: 

GSEA code: 

MDA231_ranked_genelist_input <- MDA231_ranked_genelist$log2fc
names(MDA231_ranked_genelist_input) <- MDA231_ranked_genelist$name

H <- msigdbr(species = "Homo sapiens", category = "H")
H.gene_symbol.ls <- H %>%
  dplyr::select(gs_name, human_gene_symbol) %>%
  group_by(gs_name) %>%
  summarise(all.genes = list(unique(human_gene_symbol))) %>%
  deframe()

MDA231_gsea.H <- fgsea(pathways = H.gene_symbol.ls,
                      stats = MDA231_ranked_genelist_input)

topPathwaysUp <- MDA231_gsea.H[ES > 0][head(order(padj), n=10), pathway]
topPathwaysDown <- MDA231_gsea.H[ES < 0][head(order(padj), n=10), pathway]
topPathways <- c(topPathwaysUp, rev(topPathwaysDown))
plotGseaTable(H.gene_symbol.ls[topPathways], MDA231_ranked_genelist_input, MDA231_gsea.H, 
              gseaParam=0.5)

Best wishes, 

Leo

[David Eby]

Hi Leo,

The code that you have sent is for fgsea, which is an independent implementation and not something we built or can directly support.  I would suggest you reach out to them at the GitHub location listed on their Bioconductor page.

Alternatively, you could try doing a similar experiment with our GSEA Desktop in Preranked mode and see how that works out.

Regards,

David

David Eby
www.gsea-msigdb.org
igv.org
genepattern.org

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