I have several GO lists derived from differentially expressed genes. The GO terms are almost identical across the lists, however, the number of a given GO term and FDR value are different. I was wondering how I can appropriately compare the GO terms among the lists. For comparing the number, I did a statistical test to find which GO terms are significantly different among the lists, and got some GO terms, please kindly let me know if it's a right approach? however, there are some GO terms that their number aren't different among the list, but their FDR are different, for example, please consider the below GO term:
Number in input list Number in reference FDR
list1 GO:0006820 68 266 7.40E-05 list2 GO:0006820 65 266 0.048
Please kindly tell me if this difference is important and has a biological meaning or interpretation? If your response is positive, could you please help me out how I can compare the given GO terms of several lists in term of FDR?
Thank you in advance