Human and Macaque Transcriptomes: A Comparison


The initial deciphering of entire genomes from several mammalian species including human, chimpanzee and macaque has now been accomplished and the massive datasets are publicly available in the form of high‐quality draft sequences. As a direct result, the development and commercialization of an ever‐increasing number of sensitive tools to measure global gene expression (the ‘transcriptome’) is providing unique opportunities to evaluate and compare biological systems. One particularly important application is to use tissues derived from macaque models of toxicity and disease to infer responses in their human counterparts. Understanding the similarities and differences in how macaques and humans respond, at the functional genomic level, to perturbations in their environments has significant relevance in biomedical research.

Keywords: macaque; microarray; transcriptome; gene expression; genome

Figure 1.

Distribution of coding and noncoding sequence similarity between macaque and human. A histogram showing the degree of nucleotide sequence similarity between macaque and human for coding (dark bars) and noncoding (3′ UTR, light bars) transcribed sequence. Sequences (n=1180) were selected that cross a well‐defined stop codon and that provide concurrent sampling of 150 bp of sequence both proximal and distal to the stop. The best human match for each macaque sequence was identified using MEGABLAST. The high‐quality subset of these data (composed only of contiguous stretches of phred Q⩾20 bp, n=633) is plotted for both coding (squares) and noncoding (diamonds) sequence. Reproduced from Magness et al..

Figure 2.

Principal component analysis of primate whole blood tissue gene expression profiles. Gene expression levels for 54 000 probe pairs (representing 38 500 genes) were uploaded to Partek Pro 6.0 and analysed by principal component analysis (PCA). The GeneChip Operating System (GCOS) normalization algorithm (A, B) and the robust multiarray averaging (RMA) normalization algorithm (C, D) are shown for comparison. The ellipsoids (B, D) represent a two‐standard deviation space from the mean of each sample set. The axes correspond to principal component 1 (PC1, x‐axis), PC2 (y‐axis) and PC3 (z‐axis). Reproduced by permission of Dillman and Phillips .



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Walker, Stephen J(Jul 2008) Human and Macaque Transcriptomes: A Comparison. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0020771]