First of all, sorry for this too broad question, I need some idea from your points of view..

I am working on a Microarray expression data, I have done number of regular analysis , and find out which signaling networks are more active between time points in my experiment, and now I have a set of signaling pathways that have been proved for their involvement in cell fate determination. ( Note: stem cell decide to differentiate or stay in their pluripotent status we simply call it "cell decision making process"). and now I would like to understand which genes or/and signaling pathways are most critical in this process, I mean by having the name of couple of signaling pathways and their genes, how I could answer this question " how these pathways interact with each other and which genes in those pathways are most critical for cell to make decision ?" Is you guys have any idea of the process that I can follow and then find those genes and create a networks of those genes then interfere this network to show how couple of genes control this process ?