So, I have a research topic for understanding the differentially expressed genes from RNA-seq. I want to see the cause of DE genes from gene regulatory point of view. It means I want to check every TF of those DE Genes and find the candidate for "responsible" TF which probably cause the DE genes. To do that, I plan to use Gene regulatory transcriptional network. I have several question regarding those network.
1. I find it there are many website which provides TF database but I find it the source is either prediction, manuscript data mining, or manually curated. My question : is those database reliable to use? (considering many things, ex: that different cell lines probably have differenty regulatory process, incomplete database, ...) Also, is those GRN database is representing the actual regulatory process because I found it is really hard to use and for several genes I know, I can not find it in the database. I am imagining a database which I can just type the gene name and list of TF of that gene appear. I found it gene card website is like that but there is no API to do it automatically.
2. I find there are many algorithm to reverse engineer GRN. Is this technique is acceptable enough? Most of the algorithm use gene expression data to reverse engineer GRN. I find it weird because I want to use GRN as a "map" to understand eexpression data. It would be strange if I use the expression data to generate GRN and then use that GRN to explain the expression result. Because of this problem, I prefer to use "existing" published GRN data but back to question no. 1.
3. My other option is to develop my GRN by myself using existing algorithm, either prediction algorithm from TFBS or gene expression (I plan to use another dataset with same cell line). My question; is the algorithm reliable enough so that I can actually use GRN to explaining my actual dataset.
Because my research is not in the GRN itself bbut rather use it, I need it to be precise enough or my explanation result has no meaning. Maybe you can also share your knowledge or experience in this area. I am really grateful if anyone can share their opinion.
*ps : I already read almost all question related to GRN in biostar but I still can not understand. Mostly because the answer is only give a database name and too many database out there. I am confused from where I need to start because it seems using 1 of the database itself is quite hard.