I have ChIP seq data of 5 TFs and I want to construct a transcriptional regulatory network between these TFs.
The approach I am using is, "If a TF is bound to a regulatory region of gene encoding one of the other TF, an edge is drawn between these two TF's, originating at the TF protein and pointing towards the bound gene". (Niu et al, 2011, Genome Research)
The window I had used to find regulatory region of gene bound to an TF is -250 bp +250 bp (is it too much or too less or if you will change this what will you keep as the window size? and why?)
Is there any other approach for the same which is simpler and more straight forward (for constructing network)?
Thank you for your time.