Fig. 1

Screenshots from MONGKIE for GBM-altered network and core gene modules. a User interface for network clustering (top left), visualization of a network and clusters (center), and expression levels in 4 GBM subtypes (top right). b EGFR-PI3K signaling module. This module is defined as a group node in the main network (shown in pink circle in a). c DNA damage response and cell cycle module (group node in blue circle). Altered and linker genes are represented by circle and diamond nodes, respectively. The alteration frequency and expression correlation were mapped to the node size and the edge width, respectively. The node color shows the average gene expression in GBM patients of mesenchymal subtypes (a) and log₂(FoldChange) between tumor vs. normal condition in all GBM patients (b and c). In a, patient groups can be switched manually in the bottom panel or automatically to show animated pictures