Arabidopsis subnetwork controlled by C, N or CN. The different genes and functional associations between them were uniquely labeled and combined into a single network graph. Protein-coding genes, miRNAs, or metabolites are represented as nodes, and color and shapes have been assigned to differentiate them according to function. Edges connecting the nodes represent the different types of biological associations (for example, enzymatic reaction, transport, protein-protein interaction, protein-DNA interaction) and are colored and labeled accordingly. The current version of this Arabidopsis multinetwork includes 6,176 Arabidopsis genes, 1,459 metabolites (7,635 total nodes) and 230,900 total interactions (edges). We used the open-source Cytoscape software  to visualize and query the molecular network for attributes of interest. We used these integrated data as a scaffold on which to analyze the various modes of regulation described above. Because all connections in the network are labeled, the evidence connecting any two nodes or subregions in the network can be readily evaluated. Bold lines represent clusters identified using Antipole (see text for more details). See Figure S3 (in Additional data file 2) for a larger version of this figure.