A supernode network summarizes the biological processes regulated in wild-type and misregulated in cli186 by L/C treatments. Supernodes are created by collapsing genes into a category according to both their metabolic pathways and the first two words of their gene annotation. This supernode network was created from the large multinetwork analysis that contains the 966 L/C regulated genes in wild-type [see Additional file 6]. Blue nodes represent biological processes that contain genes that are under wild-type L/C regulation in wild-type and cli186. Yellow nodes represent biological processes in which at least one gene shows L/C misregulation in cli186. The size of the node indicates the number of genes within that particular biological process. Nodes are connected by either metabolic (grey lines), DNA:protein (red lines = positive correlation; green lines = negative correlation) or protein:protein (blue lines) interactions.