Question: About Gene Transcriptional Regulatory Network
gravatar for bharata1803
5.2 years ago by
bharata1803470 wrote:


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.

genome • 1.5k views
ADD COMMENTlink modified 5.2 years ago by rioualen450 • written 5.2 years ago by bharata1803470
gravatar for rioualen
5.2 years ago by
rioualen450 wrote:


There are indeed many databases out there. First thing you wanna check is what organism(s) they contain. Some contain human data, some focus on model organisms, others on mice & rats... And some focus on specific TFs or TF families.

Secondly, many databases are redundant, and none of them is exhaustive. You might wanna aggregate several databases to build your network, but keep in mind you'll never get a complete information about what's going on out there.

From what I know, unfortunately it's very difficult to assess the reliability of the info, except you can assume that experimental data > manual curation > prediction...

If you're looking for human data, you can at least check these databases: TRED, ITFP, Transfac (this one's not entirely free though), Pazar, ORegAnno... They all provide downloadable data that you can parse easily.

Good luck.

ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by rioualen450

Thank you for your reply. I will check those database one by one. Well, you are right, we still don't have complete figure about gene regulation process. 

ADD REPLYlink written 5.2 years ago by bharata1803470
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