this is potentially a very broad (and maybe a bit subjective) question, if you want I agree to treat it as a community-wiky. I am searching for TFBSs on a list of putative regulatory sequences from the Xenopus genome. I am using MEME Suite's FIMO. The problem is that, despite the strong support from the presence of the TFBS arising from our wet-lab experience, I am not able to obtain FIMO q-values under the desired threshold (0.05).
In general, what are good strategies to strengthen the validity of the data used in such experiments?
What comes to my mind is:
a) use data with a robust biological background;
b) use as short as possible strings;
c) carefully mask undesired signals;
d) use a PSWM as robust as possible;
e) set the algorithm's parameters properly.