Building a network from a gene list using the GeneMANIA module in Cytoscape 2

Hello from GenomeSpace! In this video step, we will build a network from a gene list using the GeneMANIA module in Cytoscape. Make sure you have already loaded a network into Cytoscape. Click and drag to highlight and select all the nodes in your window. Right-click the Gene ID list and choose “Select All” from the context menu. Right-click the ID list again and select “Copy”. Head to the “Plugins” menu and go to “GeneMANIA” then “Search” and a new window should appear. Ensure that the organism listed matches the one from which you derived your data, in this case, “M. musculus”. Click the “Genes of Interest” textbox and paste your gene list with Ctrl+V. Some genes may not be recognized so click OK to acknowledge this. Click “Start”. If successful, Cytoscape will render a 3 dimensional network. To view the list of genes from the gene network, click on the “Genes” tab in the sidebar. If you click a network node, the corresponding gene in the list will be highlighted and information provided. Click on the “Functions” tab if you want to see the functions associated with the genes listed. Select a function to view the nodes that are associated with this functional subnetwork. Feel free to play around with all these aspects and others of the Cytoscape visualizer.

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