Another would be branch points, which are involved in the mRNA splicing process. A third example would be splice sites themselves. The first step is to collect the data. If you do transcription factors, there is already a large publicly available database. It is the transcription factor database .
Branch points are less well studied.
You can see Manny Ares about yeast branch points, but these are fairly easy and well-characterized. You might start with yeast and then try to generalize to a broader class of organisms. Characterizing human branch points seems to be an entirely open problem at present. Martin has a database of human splice sites too. There are large databases of these too.