Reference set for GO enrichment

Question

[linelr]

Hello

I have done a GO enrichment analysis on differential expressed genes, but I think that I might have used the wrong reference set: the GO annotated genome of the organism I´m doing my research on.

Now, I think that the proper reference set are the genes that were used for the differential expression analysis, because when doing the enrichment analysis, I ask if some GO terms in this particular selection of genes (i. e. DEG) are more common than would be expected by chance when they come from this particular gene set ( the collection of genes used for DE analysis.

Btw, I have used an RNA seq pipeline do obtain the genes for the DE analysis.

If anyone have the time to comment on this, I would appreciate it. Thanks in advance.

Line

Answer 1

[WouterDeCoster]

Indeed, the genes to include in your enrichment analysis are those which you could or can detect in your assay. For RNA-seq this means all genes for which you counted reads (or perhaps those above a cut-off to remove very low counts).

This is an interesting article discussing biases in enrichment analysis: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0761-7

[linelr]

thanks!

and thanks for link to the paper.