Add custom reference set/background list in command-line execution of ClueGo-Cytoscape PlugIn

[nivedas...@gmail.com]

I am using the Cytoscape plugin ClueGo to perform functional enrichment for genes in a network. I’ve been able to implement this through command line using CyREST with python by selecting certain ontologies as reference set for the enrichment. I would like to now use a custom reference/background list to perform functional enrichment. I see that this can be done on Cytoscape by changing the reference set option to ‘Custom Reference Set’ and uploading a file.

1. Should the file be a list of genes/proteins that I would like the functional enrichment to be based on?
2. How would I implement it through command-line using cyREST? I would like to point to a file in my local directory to use as background through cyREST.

[Bernhard]

Hi Niveda, here the answers to your questions:

1. Should the file be a list of genes/proteins that I would like the functional enrichment to be based on?

Yes it should be a simple list of genes/proteins without header to which you want to restrict the analysis. So this list will be intersected with all available genes from your selected ontologies and the analysis will be done on this intersecting genes   

2. How would I implement it through command-line using cyREST? I would like to point to a file in my local directory to use as background     through cyREST.

I am sorry but this feature is not implemented yet but we will work on it asap. I should not take long. In meanwhile you can test the manual version and see if it makes sense to you.

Best

Bernhard