The inferred regulatory network of Halobacterium NRC-1, visualized using Cytoscape and Gaggle. (a) The full inferred regulatory network. Regulators are indicated as circles, with black undirected edges to biclusters (rectangles) that they are members of. Green and red arrows represent repression (β < 0) and activation (β > 0) edges, respectively. The thickness of regulation edges is proportional to the strength of the edge as determined by the Inferelator (β for that edge). Interactions are shown as triangles connected to regulators by blue edges. Weak influences (|β| < 0.1) are not shown. (b) Example regulation of Bicluster 76. The four transcription factors (TFs) sirR, kaiC, VNG1405C, and VNG2476C were selected by the Inferelator as the most likely regulators of the genes in bicluster 76 from the set of all (82) candidate regulators. The relative weights, β, by which the regulators are predicted to combine to determine the level of expression of the genes of bicluster 76, are indicated alongside each regulation edge. The TFs VNG2476C and kaiC combine in a logical AND relationship. phoU and prp1 are TFs belonging to bicluster 76.
Bonneau et al. Genome Biology 2006 7:R36 doi:10.1186/gb-2006-7-5-r36