So, I've read several paper which in it, an image of gene network is present (for example : here).
So, first, I want to ask about regulatory network:
1. Is it the same as gene pathway?
2. How do I generate such a network? I assume we need a dataset which correlate between gene and the correlation is regulated/regulator gene. I already search anywhere but I can not find it. I heard FANTOM is the correct source but I don't understand how to download the relation.
What I want to do is to generate a path of transcription factor for a gene I want. I imagine like this:
Gene A has TF B,C,D.
Gene B has TF B1,B2,B3. B1,B2,B3 also has its own TF.
Gene C has TF C1,C2,C3, C4. C1,C2,C3, C4 also has its own TF.
Gene D has TF D1,D2. D1,D2 also has its own TF.
With that, I can generate a graph of TF. Currently, I find the TF manually by search the gene in genecard. But, I realized for 1 gene, there are a lot of TF (for example : link) and in genecard, it has a see all link of TF which result in more TF. I don't think I can do it manually anymore so if someone can give me some clue for online accessible or downloadable data, I'm really grateful.
Also, I found several algorithms to generate GRN from expression data. What is your opinion about this? Maybe you can share your experience.
Thank you all.