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Fig. 1 Experimental workflow. A subset of 47 conserved non-coding elements (CNEs, [26]) were randomly selected (A), and tested for enhancer activity using transgenesis in zebrafish and mice (B). Transgenic expression was decomposed into major homologous anatomical terms, and systematically compared between mouse and zebrafish embryos to identify cases of differences in trans environments (C). Finally, 26 of these CNEs could be associated to putative target genes, for which endogenous gene expression data were gathered to detect changes in gene expression between zebrafish and mouse that were consistent with trans-changes between the two species (D).