I am currently doing gene annotation for ChIP-Seq. I am wondering which annotation method should I use. Should I annotate the binding region based on the nearest gene body or the nearest transcription starting site?
For instance: Gene A is a 100kb long. Gene B is 10kb down stream of Gene A. I found a binding site at the end of Gene A (eg. 90kb downstream of Gene A's TSS and 20kb upstream of Gene B's TSS). When investigating which gene the binding region will influence, should I annotate the binding region to Gene A or Gene B?
Thank you in advance for any help.