Question: Construction Of Transcriptional Regulatory Network
3
gravatar for Dataminer
8.8 years ago by
Dataminer2.7k
Netherlands
Dataminer2.7k wrote:

Hi!

I need a tutorial or a manual which explains in detail (starting from scratch) constructing a transcriptional regulatory network. An example based tutorial/manual would be an ideal one.

Any suggestions?

Thank you

gene network • 2.8k views
ADD COMMENTlink modified 8.7 years ago by Casey Bergman18k • written 8.8 years ago by Dataminer2.7k
2
gravatar for Larry_Parnell
8.8 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

This is a good question in that it is the way that some highly interesting work in systems genetics is headed. However, I am unaware of any tutorial or manual in this area. You may need to look for such from the companies that publish technical books - try Wiley, CRC, Academic Press and others. But knowing from experience how long a lag there is between submitting a chapter and seeing the book in print, I have to urge you to look at scientific articles in this field. If you need a workflow, then bioinformatics and computational biology journals are the first places to check.

I should indicate that I have heard in recent months many talks on systems genetics and regulatory networks but have heard no mention of methods or approaches being coalesced into a manual.

ADD COMMENTlink written 8.8 years ago by Larry_Parnell16k

Thanks Larry, I am finding it very difficult to find quality articles which can give an insight of building networks. Most of them give superficial view. And you are right with the book chapters. As far as talks are concerned, the presenter only talks about the model he (or his group) constructed and what can be inferred but at no point he talks about the approach or method used in constructing network. If at any point you come across an article which could be useful in answering my question, please forward it.

ADD REPLYlink written 8.8 years ago by Dataminer2.7k

Thanks Larry, I am finding it very difficult to find quality articles which can give an insight to building networks. Most of them give superficial view. And you are right with the book chapters. As far as talks are concerned, the presenter only talks about the model he (or his group) constructed and what can be inferred but at no point he talks about the approach or method used in constructing network. If at any point you come across an article which could be useful in answering my question, please forward it

ADD REPLYlink written 8.8 years ago by Dataminer2.7k
2
gravatar for Casey Bergman
8.8 years ago by
Casey Bergman18k
Athens, GA, USA
Casey Bergman18k wrote:

I would look into the resources associated with the BioTapestry project. A few years back we had some good luck automatically constructing a regulatory network for Drosophila using BioTapestry on the FlyReg database, e.g.

alt text

At the time (early 2005), I experienced some issues with optimizing layout for a network with ~1400 edges, but the project has clearly moved on since then so it probably can handle much bigger datasets than that now.

ADD COMMENTlink written 8.8 years ago by Casey Bergman18k

Impressive, I will try it in the weekend. Thank you.

ADD REPLYlink written 8.8 years ago by Dataminer2.7k

It solves problem to an extent. I hope to find a better one. Thank you.

ADD REPLYlink written 8.8 years ago by Dataminer2.7k
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