A question about under-representaed and over-represented of GO term

[bongbimit]

Dear all,

I have a question about GO enrichment analysis. I used Blast2GO to do enrichment analysis in a rna-seq transcriptome project and the results have over-represented and under-represented gene list.

I understand if there are more DE genes for a particular category, then this category is "enriched" and the associated p-value is called "over-represented", while if there are fewer DE genes for a particular category, then this category is called "depleted" and "under-represented"?

So why and how do we consider much of under-represented gene list? Because in a tutorial slide of EMBL-EBI about gene ontology, they said that:

Pay attention to under-represented GO terms - a strong under-representation of a pathway may mean that normal functioning of that pathway is necessary for the given condition
http://www.biotnet.org/sites/biotnet...april2013.pptx (slide 50)

Anyone have a clear example about this issue?

Thank you for your consideration.