Figure 1

2D and 3D Layout of the Renal Network. The renal bipartite network laid out by the Fruchterman-Reingold [18] algorithm in 2D (A), and in 3D (B) showing the relationship between 7 renal diseases (white nodes), and 747 genes (black nodes). The size of each node is proportional to the number of its connected edges so diseases with many genes have large nodes, and diseases with few genes have smaller nodes. A yellow edge represents that the connected gene is up-regulated, and a blue edge represents that the connected gene is down-regulated. The 3D network layout enables more spreading out of nodes (as shown by the greater area used by the down-regulated genes in the centre of the 3D network), but also tends to occlude node labels.