Dear everyone,

I am currently struggling with my enrichGO results.

The results per se make sense and look great. However, when I looked into the GO terms I realized that there are not so many genes annotated with those GO terms in http://amigo.geneontology.org/ One example is neutrophil degranulation (GO:0043312) has 12 entries for homo sapiens on the geneontology website. The enrichGO analysis found that 204 of my significantly different genes are in this term.

I am very much puzzled by this huge discrepancy and cannot explain why this GO term seems to have way more entries in the org.Hs.eg.db.

Can anyone explain this?

Thanks for your help!!

Best

A similar question has been asked and answered before; see this thread: Gene-GO-term relationship discrepancy between org.Hs.eg.db and geneontology.org

The bottom line is that the GO mapping data present in org.Hs.eg.db is obtained from the NCBI,and not AMIGO. See the thread above for details and code to check.