Suggestion for enrichment analysis for small microarray set.

Question

[fu_entomology]

I am working on a microarray dataset that has 860 genes in total. I did DE gene analysis, there were 60 up regulated genes and 80 down-regulated genes.

I would like to do enrichment analysis. Would it be appropriate to use over-representation analysis (ORA), or even gene set enrichment analysis (GSEA)? My concern is the 860 gene microarray is a much reduced gene set compared to whole transcriptome, and it might introduce bias. Any comments are welcome!

[Papyrus]

Well if you set as universe the 860 genes tested, not all genes in the genome, there will be no bias regarding the background. It will however probably be hard to find enrichments because of the limited background, though there's no harm in trying.