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To increase the size of an individual gene set node, double-click on the name of the gene set in the results table on the right hand side. Each time the gene set name is double-clicked, the size will increase. Since the appearance of labels depends on the size of the node, this is a way to add labels to specific nodes in the network.
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To increase the node size across the whole network or just for specific node types, please use the top menu Node => Size dialog. As shown in the Fig. below, in a bipartite network, you can change the node size for only genes (keep gene set nodes same)
