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When you click on any of the genes or interactions within the network, on the panel to the left of the network, you will see information associated with that element (either a gene or an interaction):
You can click on any of the genes in the network and use the link on the right to add this gene to your genes of interest:
or you can use the text box at the top to enter your gene of interest:
Once your network of interest gets loaded, you can use the Settings tab on the right to customize it, for example filtering out some of the edges and nodes:
By default, PCViz shows the neighborhood of your genes of interest; but when you have more than one genes, you might simply want to get the interactions that connect your genes of interest. This also reduces the complexity of the network:
PCViz can retrieve alteration frequencies from a variety of cancer studies via cBioPortal's knowledge-base. When you load a network on PCViz, you can click on the Context tab on the right panel and select a cancer study and alteration profile (such as mutations, copy-number alterations or gene expression) that you want to investigate. When you add a cancer study to your context, PCViz will immediately show alteration frequencies for genes in your network. The alteration frequency is represented by the color on each gene:
you can load multiple cancer studies as context in which case the alteration frequency is calculated across all studies in your context. You can easily enable/disable a cancer study by clicking on its name under the Context menu and the alteration frequency information on the genes will be updated accordingly:
