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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. 3. — Different expression patterns for protein-coding genes and lncRNAs. (A) Distribution of the organ in which maximum expression is observed, for protein-coding genes (pc) and lncRNAs (lnc), for mouse, rat, and chicken. Organs are color-coded, shown above the plot. We defined the sample in which maximum expression is observed based on an average expression values across replicates, for each organ/developmental stage combination (supplementary methods, Supplementary Material online). (B) Distribution of the developmental stage in which maximum expression is observed, for protein-coding genes and lncRNAs, for mouse, rat, and chicken. Developmental stages are color-coded, shown above the plot. (C) Percentage of protein-coding and lncRNA genes that are significantly (FDR<0.01) differentially expressed (DE) among developmental stages, with respect to the total number of genes tested for each organ. Left panel: differential expression analysis performed with all RNA-seq reads. Right panel: differential expression analysis performed after down-sampling read counts for protein-coding genes, to match those of lncRNAs (see Materials and Methods). (D) Distribution of the developmental stage in which maximum expression is observed, for protein-coding genes and lncRNAs that are significantly DE (FDR<0.01) in each organ, for the mouse. Percentages are computed with respect to the total number of DE genes in each organ and gene class.