[Bio-software] Please recommend good ontology analysis tools

RY Bao via bio-soft%40net.bio.net (by ry_bao from yahoo.com)
Thu Jul 29 19:29:10 EST 2010

Hello Everybody,

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)


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