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The normalized gene expression data for mouse and frog were downloaded from the functional landscape of mouse gene expression website (http://hugheslab.med.utoronto.ca/Zhang) and the Conservation of Core Gene Expression in Vertebrate Tissues: Supplementary Data website (http://hugheslab.ccbr.utoronto.ca/supplementary-data/vertebrate_expression), respectively.
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Orthologous genes for mouse (Mus musculus), chicken (Gallus gallus), and frog (Xenopus tropicalis) were downloaded from Ensembl.
For the two transcriptome-sequenced ranid frogs (Rana chensinensis and Rana kukunoris), sequencing reads were downloaded and processed using Trinity to assemble the transcripts, after which Transdecode was used to extract CDS and protein sequences.
Whole-genome assemblies of anole lizard, western clawed frog, zebrafish, fugu, green spotted pufferfish, medaka, and stickleback were downloaded from Ensembl (Hubbard et al. 2009).
Genome sequences were downloaded from UCSC GoldenPath database for the 7 species: human (hg18), mouse (mm7), rat (rn4), chicken (galGal2), frog (xenTro2), zebrafish (danRer3), tetraodon (tetNrg1) and fugu (fr1).
SNP lists were downloaded from their websites.
Protein sequences were downloaded from IMG [40].
were downloaded.
The phastCons score database [ 37] of 9 species (rat, mouse, human, dog, cow, opossum, chicken, frog, and zebrafish) conservation was downloaded from the UCSC genome browser [ 38].
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