Figure 3

Networks depicting putative gene interactions based on the occurrence of overrepresented motifs in the UCR of DEG between A. mellifera castes. (A) Bipartite graph representing the occurrence of motifs (colorized circles) in the UCR of DEG in queen and worker castes. Motifs represented in blue were found in the functional group "JH responsive" (M6-3-1, M6-3-2, M6-3-3) and "hormone+caste" (M7), those in green were found in the functional group "apoptosis/other proteins" (M4-2), in yellow in top10-WL4 genes (WL4-1, WL4-2, WL4-3) and in magenta are motifs found experimentally in other insects (CF1-USP and EcR-USP). The black arrows point to genes coherently up-regulated in caste stages and JH assay. Genes with unknown function are marked by a question mark (?). Genes marked by an asterisk (*) were not in the training dataset for motif discovery. The worker DEG marked by a hash (#) are usp, crc and RfaBp, repressed by hormones. The queen DEGs marked by a hash (#) are tor and trap1, negative regulators of cell death in response to nutritional availability. (B) One layer graph (subsumed) designed to obtain measures of complex networks. Clustering coefficient (cc) and degree (d) show that worker's network (d = 62.21 ± 28; cc = 0.37 ± 0.23) is more interconnected than queen's network (d = 31.23 ± 15.67; cc = 0.36 ± 0.25). This suggests the worker DEGs share much more conserved cis-elements when compared to queen DEGs. (C) A plot obtained by representing each motif by a point with abscissa equal to its degree in the queen network and the ordinate equal to its degree in the case of the worker network. The fact that most nodes resulted above the main diagonal line (represented by the dashed line) objectively indicates that most promoters, except for "hormone" and "apoptosis" motifs, regulate more genes in the latter case (workers).