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This article is part of the supplement: Proceedings of the 23rd International Conference on Genome Informatics (GIW 2012)

Open Access Proceedings

Natural selection drives rapid evolution of mouse embryonic heart enhancers

Ben-Yang Liao* and Meng-Pin Weng

Author Affiliations

Division of Biostatistics & Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan Town, Miaoli County 350, Taiwan, ROC

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BMC Systems Biology 2012, 6(Suppl 2):S1  doi:10.1186/1752-0509-6-S2-S1

Published: 12 December 2012

Additional files

Additional file 1:

Supplementary figure S1. Evolutionary rates of enhancers. Rates of evolution calculated for mouse enhancers of embryonic forebrain (FB), midbrain (MB), limb (LM), and heart (HT), included D (A), normalized evolutionary rates D/d4 (B) or D/di (C), and neutral substitution rates d4 (D) or di (E). The values of upper quartile, median, and lower quartile are indicated in each box, whereas the bars outside the box indicate semi-quartile ranges. D, D/d4, D/di, d4 and di were computed based on mouse-human alignments. Pairwise comparisons showing significant differences in D, D/d4, D/di, d4, or di are connected with gray lines (Mann-Whitney U test).

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Additional file 2:

Supplementary figure S2. Evolutionary rates of enhancers. Rates of evolution calculated for mouse enhancers of embryonic forebrain (FB), midbrain (MB), limb (LM), and heart (HT), included D (A), normalized evolutionary rates D/d4 (B) or D/di (C), and neutral substitution rates d4 (D) or di (E). The values of upper quartile, median, and lower quartile are indicated in each box, whereas the bars outside the box indicate semi-quartile ranges. D, D/d4, D/di, d4 and di were computed based on mouse-rat-human multiple alignments. Pairwise comparisons showing significant differences in D, D/d4, D/di, d4, or di are connected with gray lines (Mann-Whitney U test).

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Additional file 3:

Supplementary table S1. The proportions of enhancers that underwent selection based on mouse-human alignments (neutral reference: fourfold degenerate sites)

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Additional file 4:

Supplementary table S2. The proportions of enhancers that underwent selection based on mouse-human alignments (neutral reference: intron sites)

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Additional file 5:

Supplementary figure S3. Enhancers with a highly expressed adjacent gene evolve more rapidly. Evolutionary rates are represented by D (A) or D/d4 (B). Gene expression level was defined by the maximum expression signal of the 61 mouse tissues. Spearman's rank correlation coefficient is (C) 0.044 (P <10-4) and (F) 0.042 (P <10-3) for the unbinned data. The values of upper quartile, median, and lower quartile are indicated in each box, whereas the bars outside the box indicate semi-quartile ranges. Pairwise comparisons showing significant differences in D or D/d4 are connected with gray lines (*0.01<P≦0.05 and ***P≦0.001 by Mann-Whitney U test).

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