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Genetics. Oct 2003; 165(2): 747–757.
PMCID: PMC1462792

Mixed-model reanalysis of primate data suggests tissue and species biases in oligonucleotide-based gene expression profiles.

Abstract

An emerging issue in evolutionary genetics is whether it is possible to use gene expression profiling to identify genes that are associated with morphological, physiological, or behavioral divergence between species and whether these genes have undergone positive selection. Some of these questions were addressed in a recent study (Enard et al. 2002) of the difference in gene expression among human, chimp, and orangutan, which suggested an accelerated rate of divergence in gene expression in the human brain relative to liver. Reanalysis of the Affymetrix data set using analysis of variance methods to quantify the contributions of individuals and species to variation in expression of 12,600 genes indicates that as much as one-quarter of the genome shows divergent expression between primate species at the 5% level. The magnitude of fold change ranges from 1.2-fold up to 8-fold. Similar conclusions apply to reanalysis of Enard et al. 2002 parallel murine data set. However, biases inherent to short oligonucleotide microarray technology may account for some of the tissue and species effects. At high significance levels, more differences were observed in the liver than in the brain in each of the pairwise species comparisons, so it is not clear that expression divergence is accelerated in the human brain. Further, there is an apparent bias toward upregulation of gene expression in the brain in both primates and mice, whereas genes are equally likely to be up- or downregulated in the liver when these species diverge. A small subset of genes that are candidates for adaptive divergence may be identified on the basis of a high ratio of interspecific to intraspecific divergence.

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Selected References

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  • Brunet Michel, Guy Franck, Pilbeam David, Mackaye Hassane Taisso, Likius Andossa, Ahounta Djimdoumalbaye, Beauvilain Alain, Blondel Cécile, Bocherens Hervé, Boisserie Jean-Renaud, et al. A new hominid from the Upper Miocene of Chad, Central Africa. Nature. 2002 Jul 11;418(6894):145–151. [PubMed]
  • Cavalieri D, Townsend JP, Hartl DL. Manifold anomalies in gene expression in a vineyard isolate of Saccharomyces cerevisiae revealed by DNA microarray analysis. Proc Natl Acad Sci U S A. 2000 Oct 24;97(22):12369–12374. [PMC free article] [PubMed]
  • Cheung Vivian G, Spielman Richard S. The genetics of variation in gene expression. Nat Genet. 2002 Dec;32 (Suppl):522–525. [PubMed]
  • Chu Tzu Ming, Weir Bruce, Wolfinger Russ. A systematic statistical linear modeling approach to oligonucleotide array experiments. Math Biosci. 2002 Mar;176(1):35–51. [PubMed]
  • Enard Wolfgang, Khaitovich Philipp, Klose Joachim, Zöllner Sebastian, Heissig Florian, Giavalisco Patrick, Nieselt-Struwe Kay, Muchmore Elaine, Varki Ajit, Ravid Rivka, et al. Intra- and interspecific variation in primate gene expression patterns. Science. 2002 Apr 12;296(5566):340–343. [PubMed]
  • Gu Jianying, Gu Xun. Induced gene expression in human brain after the split from chimpanzee. Trends Genet. 2003 Feb;19(2):63–65. [PubMed]
  • Jin W, Riley RM, Wolfinger RD, White KP, Passador-Gurgel G, Gibson G. The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster. Nat Genet. 2001 Dec;29(4):389–395. [PubMed]
  • Kerr MK, Martin M, Churchill GA. Analysis of variance for gene expression microarray data. J Comput Biol. 2000;7(6):819–837. [PubMed]
  • Li C, Wong WH. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proc Natl Acad Sci U S A. 2001 Jan 2;98(1):31–36. [PMC free article] [PubMed]
  • Oleksiak Marjorie F, Churchill Gary A, Crawford Douglas L. Variation in gene expression within and among natural populations. Nat Genet. 2002 Oct;32(2):261–266. [PubMed]
  • Quackenbush John. Microarray data normalization and transformation. Nat Genet. 2002 Dec;32 (Suppl):496–501. [PubMed]
  • Rifkin Scott A, Kim Junhyong, White Kevin P. Evolution of gene expression in the Drosophila melanogaster subgroup. Nat Genet. 2003 Feb;33(2):138–144. [PubMed]
  • Sásik R, Calvo E, Corbeil J. Statistical analysis of high-density oligonucleotide arrays: a multiplicative noise model. Bioinformatics. 2002 Dec;18(12):1633–1640. [PubMed]
  • Wolfinger RD, Gibson G, Wolfinger ED, Bennett L, Hamadeh H, Bushel P, Afshari C, Paules RS. Assessing gene significance from cDNA microarray expression data via mixed models. J Comput Biol. 2001;8(6):625–637. [PubMed]

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