Given a set of bound regions for transcription factor identified by ChIP-chip or ChIP-seq, how do you find the regulated target gene?
AFAIK, the method of choice seems to answer this question seems to be the ad hoc approach to "find the nearest gene or TSS", as implemented in the ChIPpeakAnno Bioconductor package. But since cis-regulatory elements can skip over "bystander" genes and act on non-neighboring genes, clearly something more sophisticated is needed to generate better target gene assignment.
I've seen one paper that integrates (i) distance to genes with (ii) expression data from knockout studies and (iii) prior data to prioritize target genes for bound regions, but there is no code available on their webpage. This group does provide a web application to store and browse target gene assignment, but I was hoping to find additional code that does this automatically. Additional papers outlining strategies that can solve this task would be welcome as well.