Protein atlas networks in cytoscape

Question

[lirgafny]

Hi, I wish to generate a similar network as presented in the Protein Atlas papers for my own dataset. In their networks, instead of showing the genes that connect between the nodes (cell types, organ, etc.), they show the number of shared genes that connect between the different nodes. When I import their publicly available networks from NDEx (for example - The Human Protein Atlas - Blood) I saw that the nodes include the "cell" and the "gene" and not only the "cell" . I wish to understand how to move from this type of network visualizations of the one shows eventually in the paper - https://science.sciencemag.org/content/366/6472/eaax9198 (in fig 5c). Thanks a lot Lir

Answer 1

[scooter]

Hi Lir, Unfortunately, I don't know of an easy way to get from the network of cells and proteins to a network just of cells with counts on the edges. My knee-jerk would be to export the data as a table and then process the table using python or some external program to give a new network with a count of shared genes. Sorry I couldn't be of more help.

-- scooter