Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome

Additional data file 1:

Supplementary Text 1 describes the dependence of conservation rates on the methods employed. Supplementary Text 2 provides a note on some further properties of the BRPR score. Supplementary Figure 1 illustrates the behavior of BRPR scores in mammalian comparisons as the window of examined upstream sequence is reduced. Supplementary Figure 2 reproduces some of the information in Figure 2 (main text), but includes error bars in order that statistical significance of our analysis may be judged. Supplementary Table 1. A shows conservation rates of 5 kb upstream regions and TFBSs as found by the DNA Block Aligner (DBA)-based analysis. Supplementary Table 1. B shows conservation rates of 5 kb upstream regions and TFBSs, as found by the UCSC multiple alignment-based analysis. Supplementary Tables 2 to 9 show TFBS conservation dependency on transcription factor identity for human sites conserved in other species (based on UCSC multiple alignment analysis). Supplementary Tables 10 to 17 show TFBS conservation in relation to the GO category of the regulated gene for human sites conserved in eight other species (based on UCSC multiple alignment analysis). Supplementary Table 18 provides conservation rates of 5 kb upstream regions and TFBSs for human compared with 218 combinations (₈C₅) of the eight other tested genomes (based on UCSC multiple alignment analysis). Supplementary Table 19 provides a re-analysis of 5 kb upstream coverage rates and regulatory site conservation using only those sites/regulated genes stored in TRANSFAC public (v. 7.0).

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