I just got the output files of the BETA-plus analysis. I just would like to know what are the difference between each parts of the motif analysis.
I am wondering what is the difference between "PART1: UP TARGET GENES" and "PART4: UP VS NON TARGET MOTIF"? Also, in "PART3: UP VS DOWN MOTIF SCAN", is it a positive T score means the motif is more associated with the unregulated targets? I got some motif only listed in "PART1: UP TARGET GENES", but they are not listed in "PART3: UP VS DOWN MOTIF SCAN".