Gene Coexpression Network Construction

Question

[K. Bedejova]

Hi! I would like to construct a gene coexpression network that I could use for further analysis, like community detection/detecion of functional gene modules in that network. Could anyone please share materials how to construct a gene coexpression network, some code examples maybe ? Thanks very much in advance.

[Arindam Ghosh]

As ATPoint mentioned you should first look into established packages. They usually have a well explained tutorial. Apart from that a simple Google search can bring out several other tutorials. One such is Step-by-Step Construction of Gene Co-expression Networks from High-Throughput Arabidopsis RNA Sequencing Data.

Answer 1

[ATpoint]

Hi K. Bedejova, you should check the established packages for this such as WGCNA and then ask specifically for help once you get stuck. People are typically reluctant to provide step-by-setp help if you have not invested any effort yourself.

Answer 2

[Kevin Blighe]

Another one (not published): Network plot from expression data in R using igraph

Kevin