Example of using Cytoscape to visualize gene interaction networks.
Given a gene interaction table where total mutations is found at a gene’s intersection with itself and gene co-mutations in the remaining columns, we parse into Cytoscape compatible, tab-delimited tables using Python. The output from the script is imported into Cytoscape 3.0.2 generating the interaction network.
In the saved Cytoscape session, we removed genes with fewer than 5 total mutations bringing the count from 423 genes with 9317 interactions down to 46 genes with only 596 interactions. Organizing the layout was done using edge-weights based on co-mutation rates between genes. Node size corresponds to a gene’s total mutations while node color corresponds to a nodes relative centrality score. Genes in the center are colored red; the periphery are green.
pip install toolshed