Hi, I'm struggling to figure out how to go from gene expression data to  be able to create a network out of the most expressed genes in a cell line. Ok, I have developed an application for Cytoscape where I want to compare my analysis with research on the NCI-60 cell lines. My goal is to do these steps:

1: Use one of the cell lines in the NCI-60 cell lines, in my case I will use the NCI_H23 where there is 3 samples in this dataset.

2: Use the most expressed genes in the NCI_H23 cell line to create a subnetwork using a protein interaction network database like iRefIndex, etc.

After these two steps I should finally be able to upload the network to Cytoscape and perform my analysis, but being a programmer  I'm kind of stuck. I have tried using one of the 3 samples where I mapped the Affymatrix IDs to gene symbol and then selecting the top 20% genes with the highest values using a cutoff value, but I'm not sure if this is the correct way to do it and I'm not sure how to do step nr.2 above if my list of genes is correct.

I would really appreciate help on this as I've been stuck on this for over a week now.