Dear All,

I have a set of up- and downregulated miRNAs from which I have obtained two lists of possible up- or downregulated target genes (merging three online prediction databases). Of these predicted targets, I would like to build a network in Cytoscape, keeping for each set the selected colors (i.e. red->upregulated, green->downregulated). The problem is that when I try to merge the two Largest Subnetworks in Cytoscape, the predicted proteins do not retain the selected colors, but all becomes uniform. I would like also to create and analyze the entire network using MCODE, keeping always the distinct colors, but I don't know how to do it.

Do you have any idea/protocol that I can follow?

Thank you in advance!

Alessandro