We all know that through ChIP-seq experiments a lot of binding sites are identified for a transcription factor but the major question which remains(or atleast for me) is that, how many of these ChIP-seq sites are functionally inportant?
So for instance if you have a transcription factor binding sites identified from a ChIP-seq experiment and this TF binds mostly in promoter (as the sites identifiedd are present in promoter regions). How can one identify the functionally important sites for this transcription factor out of the number of sites identified through ChIP-seq experiment. Also, if one has the availability of RNA-seq data how this data can be efficiently be coupled with ChIP-seq to aid the identification of potential functional regions.
Please share your experience and logic that you would choose for the given set of data and also if you have across some articles please share.