How to select GO terms once you've calculated ontologies?

Question

[Juan Cordero]

Dear community,

I am a newbie in GO enrichment analysis. I have done a enrichment with several methods: classicScore with KS and classicCounts with Fisher method. Now I have got a table with the ontologies sorted by Fisher p-values. Which method should I use to sort the terms?

And now the main question: once I have a list of relevant go terms, it may happen some of them are parents of others, and so should I discard all the parents and consider only the leaves of the tree?

Answer 1

[Jean-Karim Heriche]

Typically, GO terms are selected by setting a threshold on the p-values (corrected for multiple testing). To deal with the ontology structure, I like the method described in Barriot et al, BMC Bioinformatics 2007,8:332.