We used (for duplicate data):
p3 cutoff <= 0.0001; p1 cutoff <= 0.0001;
neighbor <= 0.05 and 2 of 3 <= 0.0005

For USF1 we used YLE defaults:
p3 <= 0.001; p1 <= 0.001;
neighbor <= 0.1 and 2 of 3 <= 0.005

For CREB we used:
p3 <= 0.001; p1 <= 0.015;
neighbor <= 0.1 and 2 of 3 <= 0.005