Figure 3

Functional relationships between broken, amplified and deleted candidates drivers in adult-type GCTs. a. Hierarchical clustering of the expression levels of the 5 broken genes (purple), 13 amplified (red), 7 deleted candidate drivers (green), and FOXL2 in the 10 GCTs (see details in Methods). The clustering defines three groups of genes. The first group contains 5 deleted putative drivers together with the majority of broken genes, amplified MMAB and FOXL2. The second group includes almost all amplified genes, and one broken and 1 deleted genes. Amplified TSPAN32 (anti-correlated to other amplified genes) defines a separate group along with the remaining broken gene. b. Physical interaction network involving the proteins encoded by broken, amplified or deleted candidate drivers and common binding partners. Known interactions were retrieved automatically by DAPPLE v2.0 (http://www.broadinstitute.org/mpg/dapple/dappleTMP.php, see [48]), using default parameters. The network was manually reorganized to highlight the expected hub position of AKT1 and the partition of identified binding partners in signaling and transcription regulation. Gene set enrichment analysis was performed with Enrichr, for the 43 genes depicted in the network (the displayed p-values are Bonferroni-corrected).