I sometimes receive a BED file as a result from some experiment (for example peak list of some factor) and try to figure out if and what is special in these regions. Is there a "common denominator"? So I am checking for motifs, GO/Pathway of nearest genes, enrichment in, say, enhancers, comparison with TF ChIP-Seqs etc...This is not systematic and definitely non exhaustive.
Can anyone suggest a tool, set of tools, pipeline or even a paper that tries to address this, less-than-well-defined challenge in a systematic manner? The goal is to stay objective and detach the pipeline from the original reasoning behind the creation of the BED file.