Network generation with calculated distance metrics

Question

[Farshad]

Hi everybody,

This is my first question here! Hope I can manage it to work.

This is my case: I have a list of a number of genes, in pairs, and the metrics of how these pairs are connected.

For example:

A <- 2 -> B

G <- 3.5 -> H

G <- 1 -> B

2, 3.5, and 1 are distances.

If I don't want to use the data already available (like GeneMania and Ingenuity), and just want to make my de-novo network of relationships, is there any way I can do that in R? I am not very keen about clustering, network generation is preferred.

Also, maybe a resource of available methods for network generation?

Thanks for your attention.

Answer 1

[dago]

I think you can use Cytoscape http://www.cytoscape.org/ to display the network

You just need to create a network where the nodes are the genes (e.g. A,B,C) and the edges are the distances. You can prepare a table where in the First two columns you have your genes and in the third the dist. Then there are tons of package in Cytoscape to analyse the data.

Answer 2

[Farshad]

Thanks, Dago! It was very helpful. I tried it and it seems fine to me. I used the Network Analyzer app of the Cytoscape. Do you have any preferred app in Cytoscape?

[dago]

You are welcome. Not really, it really depends on what are you doing. The Cytoscape web site is really good and the packages are well explained and easy to use. Thus, if you see a package that could be useful for you, do not be afraid of give it a try! Good luck!