Using BiNGO with same gene list and settings - different results

[Leah Zagore]

Hello,

I have been trying to perform some GO analysis using BiNGO. I have been using the in-app Mus musculus annotation as the reference set. I've used the same settings and gene list in the two excel files I've attached and gotten very different results. Perhaps there is a really obvious issue that I'm missing. I've also noticed that selecting "use whole annotation as reference set" results in different "N" numbers in the output .bgo file in other analyses I've performed. Any explanations? Thank you very much for your help!

Leah