Figure 3.

Network of Ciona and mouse Slc6 paralogs and their orthology relationships. Ciona ENS_07757 has 35 paralogous genes (light gray edges), and among them, ENS_09380 and ENS_03845 are downregulated in the OC:Act condition (Supplementary Table 1), while mouse Slc6a2 has 22 paralogous genes. The two paralogous gene networks are connected not only by the orthology relationship between ENS_07757 and Slc6a2 but also by other seven relationships. Though none of the eight mouse genes that have orthology relationships with Ciona genes (red edges) are differentially expressed genes (DEGs) in the mouse Oc1/Oc2^−/− KO transcriptome, two alternative genes (Slc6a1 and Slc6a4) among their paralogs are actually DEGs in mouse (Sapkota et al., 2014). Differentially expressed genes in both Ciona (ENS_03845, ENS_07757, and ENS_09380) and mouse (Slc6a4 and Slc6a1) are shown in yellow. Light blue nodes: Ciona Slc6 paralogs (“ENS_” in the gene names is omitted); green nodes: M. musculus paralogs. The visualization was obtained with Cytoscape (Shannon et al., 2003).