Choosing right GSEA background gene sets
I need to test whether a particular gene set is upregulated in my data. First, I have to provide a sorted ranked background gene set like this:
gene_name logfc
xx 3.0
yy 2.0
I can get this ranked list from different expression analysis, but do I need to filter out insignificant genes (based on p-value or logfc) in advance? Or just provide all detected genes?
1 answer
Run on all tested genes. Here is why: Can I run GSEA on a subset of genes
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no filtering for GSEA other than filtering of low expressed genes for your differential expression analysis.
The following paper offers some additional insights: Urgent need for consistent standards in functional enrichment analysis