In many studies like This(Table1) I have seen p-values are calculated for Gene Ontology Terms. Can somebody give me numerical calculation using a small example how these p-values are calculated for GO terms?
I hope this might help - https://onlinecourses.science.psu.edu/statprogram/node/138/
They explained with an example.
Also, you can also check this previous thread discussion - How do I calculate the p-value in a gene enrichment analysis, using parametric and non-parametric methods?
Actually I have no problem understanding basics of p-value my only problem is what data here is and how they calculated p-value in this GO case particularly?
Check this article (Fig. 1c and the text related to Fig. 1c "Enrichment analysis"). If you have gene list you can use GeneSCF to calculate p-values for enriched terms for your gene list.