TopGO question: Annotated vs. Significant

Question

[ecope6]

Hello All,

Please excuse the simplicity of my question, but I need some assistance with topGO. I'm trying to decipher between "Annotated" and "Significant" in the topGO output table. In four of the columns in the table generated, the third and fourth columns read "Annotated" and "Significant" with numbers listed below each. What is the difference?

Thank you kindly,
Emily

Answer 1

[h.mon]

Not all genes from your list will have a corresponding GO annotation, and GO enrichment tests can only be performed, obviously, on GO-annotated genes. The significant genes are the the genes which you told topGO are differentialy expressed - I am guessing you are using method "Fisher".

[ecope6]

Thank you h.mon for your response. Yes, I'm using the "fisher" method. Thank you for your help.