I would like to ask you for help.
I have got the all data about gene expression from RNA-Seq method. My aim is to prepare the system network (with one the most important gene in the middle).
1) Could you tell me please what are the major steps of preparing such network from gene expression values? (I' m working mostly in R)
2) How could I know which genes are the transcript factors?
3) How could I know which transcript factors are the direct binding partners of this central gene?
I'm totally new in this thema, because of it my questions are theoretical - I just want to know how should I plan the task.
Thank you very much!