how to automatically discover the enriched submodules

[Tongjun Gu]

Hello, I got many groups of differential expressed (DE) genes and would like to find the enriched submodules in the groups of DE genes using jactivemodules. As I have many groups of DE genes, it is not possible to do it manually. Is there a way to do it automatically using linux commands without graphic interface and save the lists of genes from each submodule for downstream analysis? If not, does anyone have any suggestions? Thank you very much!

[Barry Demchak]

I think this may already have been answered on another thread ... 

In case it's not:

Hi, Tongjun --

Thanks for this good question.

We''re working on automation features like this, but we''re not there yet. Our best suggestion would be to locate a Python-based library and use that instead.

For background, there are two mechanisms for automating Cytoscape: cyCommands (for scripts) and cyREST (for application-based invocation). We intend to support JActiveModules and many other functions via either of these mechanisms, and we''re working to make this happen. Look for something like this in the next several months.

Thanks!

[Tongjun Gu]

Hi Barry,

Thanks for forwarding the useful information. Look forward to the new applications

Tongjun