Figure 5
From: Construction and use of gene expression covariation matrix
Mapping of probe set position in 3D space with Keiko. Each panel shows the configuration of nodes after attractive forces greater than 60 (A), 50 (B), 40 (C), 30 (D), 20 (E), or 1 (F) have been activated and an equilibrium obtained (network HG-U95-NR1). For repulsive forces, the threshold used to activate the forces is equal to the attractive force minus 10. Each node is allowed to move in the direction resulting from the sum of the attractive and repulsive forces, and the whole network reaches a new configuration characterized by its potential energy. When the difference in energy between two successive configurations is inferior to a given threshold, new forces with smaller values are activated. Nodes are not allowed to collapse, and repulsive forces are automatically added when the distance between two nodes is below a given limit.