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Hominoid-Specific De Novo Protein-Coding Genes Originating from Long Non-Coding RNAs

Figure 4

Non-coding orthologs of human de novo protein-coding genes in rhesus macaque and chimpanzee show tissue expression profiles similar to human.

(A) Hierarchical clustering chart of tissue expression proportions. For each gene in one species, tissue expression proportions were calculated by normalizing RPKM scores with the total expression level of the gene in that species. The scores were then clustered according to similarity using complete linkage hierarchical clustering. For each gene, cross-tissue correlation coefficients between human and chimpanzee (H–C), chimpanzee and rhesus macaque (C–R) and human and rhesus macaque (H–R) are shown. (B) Correlation coefficient scores for tissue expression profiles between human and rhesus macaque. Correlation coefficients for de novo genes (brown histograms) are illustrated with background simulated by 10,000 Monte Carlo simulations neglecting ortholog relationship for the tissue expression profile (blue histograms, mean scores are shown). (C) For each pair of tissues, Spearman correlation coefficients were computed separately and the extent of tissue-specific differences in de novo gene expressions are shown. Dotted lines highlight comparisons between pairs of corresponding tissues in different species. Grey boxes: missing data. *Correlation coefficient not available due to low tissue expressions in one or both species. #Gene reported in previous study as human-specific de novo protein-coding gene.

Figure 4

doi: https://doi.org/10.1371/journal.pgen.1002942.g004