Question: Transcription regulatory network and gene pathway
0
gravatar for bharata1803
5.0 years ago by
bharata1803450
Japan
bharata1803450 wrote:

Hello,

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 • 1.4k views
ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by bharata1803450

Hello,

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 5.0 years ago by Anima Mundi2.7k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 980 users visited in the last hour