I am very curious to know in detail, how one can build a gene regulatory networks using ChIP-seq data and RNA-Seq data. I guess a lot of people who are new to networks want to know about this.
As an example, if I have binding profile of 3 transcription factors and 2 epigenetic marks in one cell line. I also have figured out the target genes for these TFs and also for the epigenetic marks using windowing approach. and when I build a table
TF1 Nanog TF2 OCT8 TF3 RUNX1 TF1 ETO TF1 HEB TF2 HEB EM1 OCT8
and so on..... the list grows I get quite a dense network.
Now the question is how to filter this?
Is their any text that is precisely dealt with this or any tutorials online that have explicitly described such approaches?
Any help will be appreciated.