Comparison between Intact Genes and Pseudogenes

<p>(A) shows the distributions of expression divergence between humans and chimpanzees for intact genes and pseudogenes. (B) shows the distributions of the ratio of expression divergence between humans and chimpanzees and expression diversity within humans for intact genes and pseudogenes.</p

Brain and Liver Transcriptome Change among Primates as a Function of Time

<p>Average expression differences within and between primates in brains (A), in liver (B), and for genes in brain for genes with high (red) and low (blue) variation among six humans (C). Colors: red, comparisons between and with humans; blue, comparisons between and with chimpanzees; purple, comparisons between humans and chimpanzees; orange, comparisons between orangutan and rhesus macaque; black, comparisons between experimental duplicates. Vertical error bars for expression indicate 95% confidence intervals calculated by 10,000 bootstraps over genes. Divergence times are according to <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020132#pbio-0020132-Glazko1" target="_blank">Glazko and Nei (2003</a>).</p

Brain Transcriptome Change as Measured by cDNA Arrays

<p>Colors and symbols as in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020132#pbio-0020132-g001" target="_blank">Figure 1</a> except orange, which indicates comparisons between chimpanzee and both macaque species, and blue, which indicates comparisons between rhesus macaque and crab-eating macaque. Divergence times are according to <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020132#pbio-0020132-Hayasaka1" target="_blank">Hayasaka et al. (1996</a>) and <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020132#pbio-0020132-Glazko1" target="_blank">Glazko and Nei (2003</a>).</p

Transcriptome Change among Brain Regions as a Function of Evolutionary Time

<div><p>(A) Schematic evolutionary tree for six human brain regions: B.44, Brodmann's area 44; PFC, prefrontal cortex; ACC, anterior cingulate cortex; PVC, primary visual cortex; CN, caudate nucleus; and CB, cerebellum. Numbers indicate approximate divergence time in millions of years (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020132#pbio-0020132-Butler1" target="_blank">Butler and Hodos 1996</a>; <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020132#pbio-0020132-Nieuwenhuys1" target="_blank">Nieuwenhuys et al. 1998</a>).</p> <p>(B) Average expression differences among brain regions in humans (red) and in chimpanzees (blue).</p> <p>(C) Average expression differences among brain regions in <i>M. musculus.</i> Error bars for expression indicate 95% confidence intervals calculated from 10,000 bootstrap replications over genes.</p></div

Regional Patterns of Gene Expression in Human and Chimpanzee Brains

We have analyzed gene expression in various brain regions of humans and chimpanzees. Within both human and chimpanzee individuals, the transcriptomes of the cerebral cortex are very similar to each other and differ more between individuals than among regions within an individual. In contrast, the transcriptomes of the cerebral cortex, the caudate nucleus, and the cerebellum differ substantially from each other. Between humans and chimpanzees, 10% of genes differ in their expression in at least one region of the brain. The majority of these expression differences are shared among all brain regions. Whereas genes encoding proteins involved in signal transduction and cell differentiation differ significantly between brain regions within individuals, no such pattern is seen between the species. However, a subset of genes that show expression differences between humans and chimpanzees are distributed nonrandomly across the genome. Furthermore, genes that show an elevated expression level in humans are statistically significantly enriched in regions that are recently duplicated in humans