I have a list of about 6000 genes, with around 800 of them associated with gene
family expansion. I want to detect GO over/under-representation in this dataset.
I have tried GOstat (FDR Benjamini), GOToolBox (Hypergeometric, Benjamini &
Hochberg), and Ontologizer (Parent-Child-Union, Benjamini-Hochberg). However,
they gave me very different results. Could anybody give me some suggestions
about which program to use, or which model gives better results? Are there any
other recommended programs that I can use? Thank you so much! :-)
Sunny Bao (Wayne State University, US)