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. 2019 Sep 20;37(1):240–259. doi: 10.1093/molbev/msz212

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© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Fig. 9. — Per-gene estimates of expression pattern divergence between species. (A) Relationship between the per-gene expression divergence measure (Euclidean distance of relative expression profiles among organs/stages, between mouse and rat), and the average expression values (log2-transformed TPM) across all mouse and rat samples. We show a smoothed color density representation of the scatterplots, obtained through a 2D kernel density estimate (smoothScatter function in R). Red line, linear regression. (B) Distribution of the expression divergence value for all protein-coding and lncRNA genes with predicted 1-to-1 orthologs in mouse and rat. (C) Distribution of the residual expression divergence values, after regressing the average expression level, for protein-coding genes and lncRNAs. (D) Relationship between expression divergence and exonic sequence conservation (% exonic sequence aligned without gaps between mouse and rat), for protein-coding genes and lncRNAs. (E) Average contribution of each organ/developmental stage combination to expression divergence, for protein-coding genes and lncRNAs.