Figure 4

Sharing of transcriptional neighbors among amplified/deleted genes. The 20 putative drivers and FOXL2 (blue nodes) are depicted within a network with strongly correlated transcriptional neighbors (R > =0,90), either positively (blue edges) or negatively (green edges). The diameter of the nodes reflects the number of neighbors. Amplified genes are labeled with a red a, and deleted ones with a green d. A high-resolution zoomable network is provided in Additional file 3: Figure S1. Notice that extensive sharing of transcriptomic neighbors parallels the same groups of candidate drivers than the expressional correlation in Figure 3a. Five of the deleted genes in the first group in Figure 3a share many positive and negative neighbors, and those neighbors are mainly negatively connected to the only amplified gene of this group, MMAB. The amplified genes of the second cluster (from Figure 2a) are grouped in a distinct sub-network with a connection to the dense sub-network of deleted candidate drivers restricted to C22orf26 and SPRYD3. Amplified TSPAN32 has a peculiar position, as it is connected only to neighbors of the first dense sub-network. Large grey nodes depict transcriptomic neighbors that are connected to a large portion of the candidate drivers (i.e. POU3F1, MCM9, RPL10, POLR1D, PCNA, POLA1, PI4KAP2).