Question: Transcription regulatory network and gene pathway
gravatar for bharata1803
5.6 years ago by
bharata1803490 wrote:


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.

gene genome • 1.5k views
ADD COMMENTlink modified 5.6 years ago • written 5.6 years ago by bharata1803490


probably a better way is to retrieve all TFs for all your genes from a database, e.g. Genecards, and make the graphs programmatically. However, did you try iHOP? Here is a very quick example for NANOG. What you could do, chosen a gene and a species of interest, is to look up to all relevant literature-derived sentences proposed by iHOP and select those talking about TFs directly regulating your gene.

ADD REPLYlink written 5.6 years ago by Anima Mundi2.8k
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