Integrated C. elegans data network. (A) In the visualized network, nodes represent genes and edges represent interactions between the genes. Measured fold change in gene expression was used to set the color of the nodes, green indicating up regulation, red indicating down regulation and yellow indicating no change between samples. Size of the nodes represents the number of Gene Ontology classes assigned to a gene. Query genes used to create the genetic interaction data are visualized as blue cubes. Width and spring constant of the edges represent interaction strength, and the color represents the screening method that was used to evaluate the interaction between the genes, blue for Byrne et al. and violet for Lehner et al. Because of the large number of the edges, only the edges with strongest interactions were set to visible (interaction strength > 5). (B) The hub node representing the daf-2 gene was selected and dragged to the side. Other nodes followed according to the strength of the edges as determined by the spring constant. Notice discrete groups of connected nodes representing genes directly connected to daf-2, and genes indirectly connected to daf-2. In the actual real-time simulation the movement speed and direction of the nodes are clear indications of the strength and structure of the interaction network.
Paananen and Wong BMC Systems Biology 2009 3:26 doi:10.1186/1752-0509-3-26