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Genome Res. 14:1462-1473, 2004 ©2004 by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/04 $5.00 Regional Patterns of Gene Expression in Human and Chimpanzee Brains1 Max-Planck-Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany 2 Department of Genetics, Center for Computational Genomics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, Ohio 44106, USA 3 Center for Bioinformatics Tübingen, University of Tübingen, Sand 14, D-72076 Tuebingen, Germany 4 Interdisciplinary Center for Bioinformatics, University of Leipzig, D-04103 Leipzig, Germany 5 WE Informatik, University of Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany 6 Paul Flechsig Institute for Brain Research, University of Leipzig, Jahnallee 59, D-04109 Leipzig, Germany
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.
One of the challenges in the wake of the completion of the human genome sequence is to better understand the genetic and evolutionary background of phenotypic traits that set humans apart from our closest evolutionary relatives, the chimpanzees. Such phenotypic traits include aspects of anatomy, locomotion, technology, and communication (Olson and Varki 2003
A first study of the transcriptomes of humans and chimpanzees (Enard et al. 2002
To gain a better understanding of the evolution of the brain transcriptome in humans and chimpanzees, it is necessary to analyze gene expression in different regions of the brain in multiple individuals to gauge to what extent brain regions differ in gene expression within individuals, between individuals and between species. So far, this has only been done in inbred strains of mice, wherein one study found that the cortex, cerebellum, and the midbrain differ relatively little, whereas the cerebellum was the most unique region of those tested (Sandberg et al. 2000
Patterns of Gene Expression Within Human and Chimpanzee Brains Four regions of the cerebral cortex (dorsolateral prefrontal cortex, anterior cingulate cortex, primary visual cortex, Broca's area), the central part of the cerebellum (Vermis cerebelli), and the caudate nucleus were dissected in three adult male humans and three adult male chimpanzees (Fig. 1). In addition, the premotor cortex and the area homologous to Broca's area in the right hemisphere were isolated from three humans.
Total RNA from each sample was isolated, labeled, and hybridized to Affymetrix oligonucleotide arrays containing probes to  10,000 human genes. All reliably measured expression differences within the species were summarized for each pairwise comparison and visualized in a multidimensional scaling plot for humans (Fig. 2A) and chimpanzees (Fig. 2C). Although the differences among the individuals are substantial, the caudate nucleus, the cerebellum, and the cerebral cortex regions are clearly differentiated in one dimension of the plot. In contrast, all regions of the cerebral cortex group together according to the individual from which they derive rather than according to the respective regions. This effect is particularly pronounced in humans, but also apparent in chimpanzees when the caudate nucleus and cerebellum are excluded from the analysis (Fig. 2B,D). When the expression differences within the brain are compared in the two species, the distance between the cerebellum and each of the other five brain regions studied is found to be slightly but significantly greater in humans than in chimpanzees (p = 0.015 for Broca's area, p = 0.009 for prefrontal cortex, p = 0.034 for primary visual cortex, p = 0.025 for anterior cingulate cortex, and p = 0.018 for caudate nucleus, Student's t-tests), but no significant differences are seen for any other pairs of regions (p > 0.05).
Another way to gauge the difference in gene expression within the brain is to determine the number of genes that differ significantly in expression between brain regions in all three individuals within a species (Table 1). In the cerebral cortex, the biggest difference in gene expression is between the primary visual cortex and the anterior cingulate cortex in both humans and chimpanzees, where 193 and 227 genes differ in expression in humans and chimpanzees, respectively. Many fewer differences are found among the other regions of the cortex. For example, only one gene out of the 4998 genes with detectable expression differs in expression between Broca's area and the left prefrontal cortex in all three humans analyzed and none in chimpanzees. Similarly, only four genes differ between Broca's area and its homolog in the right hemisphere in humans. Because the number of differences seen between independent experimental replicates of the same region of the brain in the same individual is one to two (data not shown), this means that we cannot reliably detect any differences among the transcriptomes of these regions. In contrast, 500–600 genes differ in expression level between the caudate nucleus and the regions of the cerebral cortex in both species, whereas 1400 genes differ between the cerebellum and the other brain regions in humans and 1200 in chimpanzees.
Region-Specific Expression Differences Next, we determined if genes with expression patterns specific to a brain region in one species also display such specificity in the other species. In Figure 3A, it can be seen that 473 genes show no difference in expression level among the four cerebral cortex regions but differ in their expression from both the caudate nucleus and the cerebellum within all three humans and/or all three chimpanzees. Of these genes, 22 genes (4.6%) show a difference in either humans or chimpanzees but not in the other species. For the caudate nucleus, 255 genes differ in one or both of the species, and three of these (1.2%) differ in only one species. For the cerebellum, the corresponding numbers of genes are 749 and 19 (2.5%), respectively. Thus, it appears that relatively more genes show species-specific expression patterns in the cerebral cortex than in the caudate nucleus or the cerebellum (p = 0.017 and 0.05, respectively, Fisher's exact test).
To investigate if this is the case, we used the full set of five Affymetrix arrays that together allow the expression levels of 40,000 transcripts to be determined to study Broca's area, the cingulate cortex, the caudate nucleus, and the cerebellum in humans and chimpanzees. Figure 3B shows that 29 and 25 genes are specific to Broca's area and the cingulate cortex, respectively, in either humans or chimpanzees or in both species. Of these, five and seven, or 17% and 28%, respectively, show specificity in only one of the two species. For the caudate nucleus and cerebellum, 794 and 2962 genes are specific to the respective regions in one or the other species, and nine and 72 genes, or 1.1% and 2.4%, in one species and not the other, respectively. Thus, the cerebral cortex differs from the other two regions of the brain in that a larger proportion of genes show region-specific expression patterns that differ between the two species.
Functional Differences Among Brain Regions Single functional groups that contain significantly more, or significantly fewer, differentially expressed genes than expected from a hypergeometric distribution were identified within each GO taxonomy (Supplemental Table 1). In the taxonomy "biological process" (Fig. 4), 18 groups of genes contain a significant excess of expression differences between brain regions, and 12 of these are associated with neuronal function, differentiation, and development in a broad sense: Eight groups are involved in synaptic transmission and signal transduction, and four are involved in cell differentiation, neurogenesis, and development, whereas one group each contains genes involved in protein phosphorylation, ion transport, and cyclic nucleotide metabolism, respectively. In contrast, of the 11 groups of genes that are significantly conserved in their expression, eight are involved in protein metabolism and transport in a broad sense. Similarly, in the taxonomy "molecular function," of 22 groups with an excess of differentially expressed genes, 19 are involved in signal transduction, ion transport, and regulation of phosphorylation or sulforylation, whereas out of eight conserved groups of genes, six are involved in protein synthesis and turn-over. The taxonomy "cellular component" contains seven groups that are significantly changed among brain regions, four of which are associated with vesicles and membranes, whereas the 13 groups of genes that are significantly conserved encode intracellular gene products. Thus, among brain regions, genes whose products are involved in signal transduction and neurogenesis are significantly more changed with respect to their expression than other groups of genes. In contrast, genes involved in protein synthesis and turn-over are significantly conserved when different regions of the brain are compared.
We used the same approach to determine whether particular functional groups of genes are over- or underrepresented among 389 genes that were differentially expressed between any two cerebral cortex regions in all three humans and/or all three chimpanzees. Although much fewer genes are considered, the distribution of differentially expressed genes across the functional groups differs significantly from the distribution of all detected genes in all three GO taxonomies (p < 0.001; Supplemental Table 2). In the taxonomy "biological process," four out of 14 groups of genes containing a significant excess of expression differences are associated with cell communication, differentiation, and development; in the taxonomy "molecular function," eight out of 12 such groups are related to signal transduction; and in the taxonomy "cellular component," all six such groups are associated with the plasma membrane and the extracellular space.
Expression Differences Between the Species
A second issue is that the extent of variation in gene expression among individuals within the species may be so large that any differences seen between the species are due to chance. To address this, we randomized the expression measurements for all genes with respect to the individual and species in which they occurred for each of the six brain regions. The results (see Methods) show that
A third issue that may complicate interspecies comparisons is that chimpanzee cDNAs differ on average at 0.8% of nucleotide positions from homologous human cDNAs (Hellmann et al. 2003  ). Because the arrays carry oligonucleotides designed to match human DNA sequences, nucleotide sequence differences between the species will contribute to apparent differences in gene expression between the species. We tested to what extent this may influence the results by using 262 chimpanzee transcripts for which the complete target sequences used for the hybridizations are known. The results (see Methods) indicate that 22% of the genes that show differential expression between humans and chimpanzees may do so because of nucleotide sequence differences between the species. A similar proportion of expression differences was suggested to be due to the differences in nucleotide sequence in other studies of gene expression in humans and chimpanzees using oligonucleotide-based microarrays (Caceres et al. 2003; Karaman et al. 2003).
Because DNA sequence differences between the species represent the major source of potential bias in the results, we used a computational algorithm that identifies oligonucleotides that hybridized inconsistently in the two species across the 16 oligonucleotides used to detect each transcript (M. Lachmann, I. Hellmann, H. Boris, and P. Khaitovich, in prep.). As implemented, this algorithm identifies 41% of human–chimpanzee sequence differences with a false-positive rate of
For each brain region, we defined an expression difference as a significant difference (p
When differences between the species found in any of the six brain regions studied in humans and chimpanzees are hierarchically clustered (Fig. 5B), it can be seen that the patterns of differences found within each region are very similar. Only the cerebellum shows several genes that differ in their expression between the species in this particular brain region and not in the other ones. This is seen also in the comparison of four brain regions with the five arrays (data not shown). Thus, a large proportion of the expression differences found between the species is not restricted to one particular region of the brain and may even be common to several different organs.
To verify this result, we reanalyzed data masking all array oligonucleotides that did not match the chimpanzee DNA sequence perfectly or where the chimpanzee sequence was unknown using all available chimpanzee DNA sequences. This resulted in a set of 3838 genes that could be reliably detected in either one or both species in at least one of the six brain regions with eight or more oligonucleotide probes. In this case, 406 genes (10.6%) were differentially expressed between the species, and 79% showed the same expression pattern difference in all six brain regions analyzed (data not shown). In addition, we compared the data collected using Affymetrix arrays with data collected by spotted cDNA arrays for six human and five chimpanzee prefrontal cortex samples (P. Khaitovich, unpubl.). Because cDNA arrays have different sources of experimental error, they can be used to verify Affymetrix data (Lee et al. 2003
Functional Differences Between Humans and Chimpanzees
Genomic Localization and Segmental Duplications
We furthermore analyzed whether expression differences between humans and chimpanzees are associated with genomic regions enriched for segmental duplications, that is, the 5% of the human genome that occurs as two or more copies with >90% similarity to each other (Bailey et al. 2001 , 2002). Table 5 shows that segmental duplications are significantly overrepresented among genes differentially expressed between humans and chimpanzees (p < 0.05, Fisher exact test). When the segmental duplications are divided into those with 90%–95%, 95%–98%, and 98%–100% sequence similarity, the overrepresentation is significant in all cases but increases with increasing sequence similarity. The most extreme overrepresentation of differentially expressed genes is observed among the duplications that are >98% identical, in which nearly 25% of all duplications that harbor genes show significant differences in gene expression. When genes were further subdivided according to whether they are more highly expressed in chimpanzee or in humans, the overrepresentation of duplicated genes is significant only for the genes that are more highly expressed in humans and not for those that are more highly expressed in chimpanzees (Table 5).
Region-Specific Gene Expression Gene expression as measured from tissue samples reflects cellular RNA levels as well as cellular composition of the tissues. Because discrete regions within the brain have different motoric, sensory, and cognitive functions, it is of interest to explore to what extent differences in gene expression can be detected between functionally different brain regions. The results show that the cerebellum differs the most from the other regions. Similar observations have been previously reported in inbred strains of mouse (Sandberg et al. 2000 ). The caudate nucleus also differs to a substantial degree from other brain regions analyzed, whereas various regions of the cerebral cortex differ little from each other. Notably, the cerebellum is the only part of the brain that shows a greater distance to the other regions in humans than in chimpanzees.
Within the cerebral cortex, we find the biggest difference in gene expression between the anterior cingulated cortex and the primary visual and primary motor cortex areas (Table 1). Interestingly, there are much fewer differences between the two primary areas, despite substantial differences in function and cytoarchitecture (Kandel et al. 2000
It may seem surprising that some cerebral cortex regions show little or no difference in terms of gene expression although they differ considerably in function (Kandel et al. 2000
Differences Between Individuals
It is noteworthy that regions of the cerebral cortex differ approximately twofold more among the humans than among the chimpanzees. Because this is not true for the caudate nucleus and the cerebellum, this is unlikely to be caused by undetected differences in RNA quality or to post mortem conditions affecting the brain as a whole. It is not likely to be caused by differences in the amount of DNA sequence variation within the species because chimpanzees carry on average more DNA sequence differences between individuals than humans (Kaessmann et al. 1999
Evolution of Brain Transcriptomes
Two previous studies have compared gene expression profiles in brains of humans and chimpanzees (Enard et al. 2002
Another observation from previous studies is that proportionally more genes have changed in the human lineage than in the chimpanzee lineage and that this acceleration in transcriptome change is specific to the brain (Enard et al. 2002
Although "interesting" hypothetical stories can be construed for many genes that are differentially expressed between humans and chimpanzees, we prefer to take a statistical approach and test by resampling (see Methods) if any of the functional groups of genes defined in the GO show an excess or lack of genes that differ in expression. When genes that differ in expression between different brain regions are tested in this way, groups of genes involved in cell communication, differentiation, and development tend to differ more than expected, whereas groups of genes involved in protein synthesis and turn-over differ less (Fig. 4). In contrast, when the genes that differ in their expression between humans and chimpanzees are analyzed, none of the three GO taxonomies shows a significant excess neither of differentially expressed genes nor of genes conserved with respect to expression. Thus, under the statistical approach used, no groups of genes stand out as changed in expression between humans and chimpanzees. This result does not support the recent claim that genes involved in neural functions and in aerobic energy metabolism are significantly up-regulated in humans relative to chimpanzees (Uddin et al. 2004
Genomic Localization and Gene Expression
Gene expression differences between humans and chimpanzees are furthermore associated with regions of segmental duplications in the human genome (Table 5). This association is seen for genes that show higher expression levels in humans than in chimpanzees, whereas there is no statistically significant association with genes that are more highly expressed in chimpanzees. Although other methodological issues cannot be precluded, the fact that segmental duplications were ascertained in the human genome and not in the chimpanzee genome is the most likely basis for this difference (Samonte and Eichler 2002 It is furthermore noteworthy that the association between interspecies expression differences and segmental duplications is greatest for the duplications that are most identical in DNA sequence (Table 5). Because duplications that arose more recently are expected to show higher sequence identity, recently duplicated genes are more likely to be associated with a difference in expression. One possible explanation may be that once a gene has been duplicated and its expression therefore increased, secondary mutations may often ensue that decrease expression to levels approximating those that existed before the duplication. Consequently, more recent duplications will show greater differences in expression between humans and chimpanzees.
Tissue Samples and Microarray Data Collection Entire brains were removed at autopsies from three male humans who were 45, 45, and 70 years old, had no history of brain-related diseases, and suffered sudden deaths without associated brain damage. Approximately 200 mg of tissue was dissected from Broca's area (Brodmann area 44, left hemisphere), Broca's area homolog from the right hemisphere (Brodmann area 44, right hemisphere), dorsolateral prefrontal cortex (Brodmann area 9, left hemisphere), premotor cortex (Brodmann area 6, left hemisphere), primary visual cortex (Brodmann area 17, left hemisphere), anterior cingulate cortex (Brodmann area 24, left hemisphere), the caudate nucleus, and Vermis cerebelli. Entire brains were similarly removed at autopsies from three male chimpanzees who were 12, 12, and approximately 40 years old. The two 12-yr-old chimpanzees were sired by the same male and the 40 yr old is unrelated to them. They had all died from natural causes, had no history of brain-related diseases, and suffered sudden deaths without associated brain damage. From these brains, the following brain regions homologous to the corresponding human regions were removed by the same neuroanatomist (T. Arendt) who dissected the human brains: Broca's area, dorsolateral prefrontal cortex, primary visual cortex, anterior cingulate cortex, caudate nucleus, and Vermis cerebelli.
Total RNA was isolated using the TRIZol reagent according to the manufacturer's instructions and purified with QIAGEN RNeasy kit following the "RNA cleanup" protocol. All RNAs were of high and comparable quality as gauged by the ratio of 28S to 18S ribosomal RNAs visualized on agarose gels and by the signal ratios between the probes for the 3'- and 5'-ends of the mRNAs of GAPDH and
Expression data were collected using Affymetrix HG U95Av2 arrays as well as Affymetrix HG U95B, C, D, and E arrays and analyzed with Affymetrix Microarray Suite v5.0 using default parameters. Arrays were scaled to the same average intensity using all probes on the array. All primary expression data are publicly available at the authors' Web site (http://www.eva.mpg.de/
Multidimensional Scaling
Differences Between the Brain Regions
Differences Between the Species
Estimating the Effect of Intraspecific Variation in Gene Expression
Estimating the Effect of Interspecific DNA Sequence Differences
Eliminating Influence of Sequence Differences Between Humans and Chimpanzees In the second approach, we identified and masked the oligonucleotide probes that differ in their binding characteristics between humans and chimpanzees as described in Lachmann et al. (M. Lachmann, I. Hellmann, H. Boris, P. Khaitovich, in prep.). Briefly, we first estimated the relative binding efficiency for each probe in the probe set by comparing the signal intensity of this probe to the intensities of all other probes within a probe set. Then we compared the calculated binding efficiencies of the probes between all human and all chimpanzee samples using a t-test. If the binding efficiency of a probe differed significantly between human and chimpanzee samples (p < 0.001), the probe was masked. Note that this algorithm does not allow the identification of genes with deletions or duplications that span the probe selection region in chimpanzees.
Functional Annotation
To assess if the overall distribution of differentially expressed genes across the groups in a GO taxonomy differs significantly from the distribution of all detected genes, we compared it with 10,000 random sets in which the same number of differentially expressed genes was randomly drawn from the annotated detected genes. For each of the 10,000 random sets as well as for the observed data, a
 2 distances in a given GO taxonomy. p-values were calculated as the proportion of random sets with a distance greater than or equal to the observed distances. We used the hypergeometric distribution to test if individual functional groups contain a significantly higher or lower number of differentially expressed genes than expected from the number of detected genes. We calculated the number of significant groups in the observed data and in 10,000 random sets of detected genes at the 1% significance level. We did not correct for multiple tests, because the global tests already suggested a significant deviation and we were interested in identifying the groups responsible for this. The percentage of false positives was estimated from the ratio of the number of significant groups in the observed data to the average number of the significant groups in 10,000 random sets. In comparisons between the brain regions, we expect 11%, 45% (at 5% significance level), and 7% false positives for the groups with significant excess and 9%, 2%, and 8% false positives for the groups with significant lack of expression differences in the taxonomies "biological process," "cellular component," and "molecular function," respectively. In comparisons between the cerebral cortex regions, we expect 13%, 12%, and 15% false positives for the groups with significant excess and 4%, 2%, and 5% false positives for the groups with significant lack of expression differences in the respective taxonomies. To find out if groups on higher levels of the GO taxonomies are significant solely because they contain significant subgroups, we removed all significant subgroups from each significant group and tested the remaining genes against the distribution of the detected genes using the hypergeometric distribution. If the group lost its significance, it was removed from further analysis. If it remained significant, the next higher group in the taxonomy was tested using the same procedure.
Genomic Localization We used overlapping sliding windows containing 21 detected transcripts to calculate the proportion of differentially expressed transcripts per window along the genome. The Y-chromosome was excluded from this analysis because very few transcripts were detected there. We simulated the random distribution by 1,500,000 permutations of the original data set with respect to the assignment of expression differences to detected genes. The p-values were calculated as the proportion of random sets that contained a number of windows with a certain ratio of differentially expressed transcripts equal to or greater than the number of windows with that ratio in the observed data.
Segmental Duplications and Gene Expression Differences
We thank A. Sajantila for help in collection of the human brain samples; R. Bontrop, W. Collignon, W. Scheffrahn, and G. Anzenberger for help in collection of the chimpanzee brain samples; K. Bauer for help in sample dissection; S. Ptak for help with statistical analysis; and M. Przeworski and M. Hofreiter for critical reading of the manuscript and many helpful discussions. We are indebted to the Bundesministerium für Bildung und Forschung and the Max Planck Society for financial support. The publication costs of this article were defrayed in part by payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 USC section 1734 solely to indicate this fact.
Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.2538704.
7 Corresponding author. [Supplemental material is available online at www.genome.org.]
Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., et al. 2000. Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25: 25–29.[CrossRef][Medline]
Bailey, J.A., Yavor, A.M., Massa, H.F., Trask, B.J., and Eichler, E.E. 2001. Segmental duplications: Organization and impact within the current human genome project assembly. Genome Res. 11: 1005–1017.
Bailey, J.A., Gu, Z., Clark, R.A., Reinert, K., Samonte, R.V., Schwartz, S., Adams, M.D., Myers, E.W., Li, P.W., and Eichler, E.E. 2002. Recent segmental duplications in the human genome. Science 297: 1003–1007.
Caceres, M., Lachuer, J., Zapala, M.A., Redmond, J.C., Kudo, L., Geschwind, D.H., Lockhart, D.J., Preuss, T.M., and Barlow, C. 2003. Elevated gene expression levels distinguish human from non-human primate brains. Proc. Natl. Acad. Sci. 100: 13030–13035.
Enard, W., Khaitovich, P., Klose, J., Zollner, S., Heissig, F., Giavalisco, P., Nieselt-Struwe, K., Muchmore, E., Varki, A., Ravid, R., et al. 2002. Intra- and interspecific variation in primate gene expression patterns. Science 296: 340–343. Finger, S. and Stein, D.G. 1982. Brain damage and recovery: Research and clinical perspectives. Academic Press, New York. Gu, J. and Gu, X. 2003. Induced gene expression in human brain after the split from chimpanzee. Trends Genet. 19: 63–65.[CrossRef][Medline]
Hellmann, I., Zollner, S., Enard, W., Ebersberger, I., Nickel, B., and Paabo, S. 2003. Selection on human genes as revealed by comparisons to chimpanzee cDNA. Genome Res. 13: 831–837.
Hsieh, W.P., Chu, T.M., Wolfinger, R.D., and Gibson, G. 2003. Mixed-model reanalysis of primate data suggests tissue and species biases in oligonucleotide-based gene expression profiles. Genetics 165: 747–757.
Kaessmann, H., Wiebe, V., and Pääbo, S. 1999. Extensive nuclear DNA sequence diversity among chimpanzees. Science 286: 1159–1162. Kandel, E.R., Schwartz, J.H., and Jessell, T.M. 2000. Principles of neural science. McGraw-Hill Health Professions Division, New York.
Karaman, M.W., Houck, M.L., Chemnick, L.G., Nagpal, S., Chawannakul, D., Sudano, D., Pike, B.L., Ho, V.V., Ryder, O.A., and Hacia, J.G. 2003. Comparative analysis of gene-expression patterns in human and African great ape cultured fibroblasts. Genome Res. 13: 1619–1630.
Kent, W.J. 2002. BLAT—The BLAST-like alignment tool. Genome Res. 12: 656–664. Lee, J.K., Bussey, K.J., Gwadry, F.G., Reinhold, W., Riddick, G., Pelletier, S.L., Nishizuka, S., Szakacs, G., Annereau, J.P., Shankavaram, U., et al. 2003. Comparing cDNA and oligonucleotide array data: Concordance of gene expression across platforms for the NCI-60 cancer cells. Genome Biol. 4: R82.[CrossRef][Medline] Lu, J., Li, W.H., and Wu, C.I. 2003. Comment on "Chromosomal speciation and molecular divergence-accelerated evolution in rearranged chromosomes." Science 302: 988; author reply 988. Navarro, A. and Barton, N.H. 2003a. Accumulating postzygotic genes in parapatry: A new twist on chromosomal speciation. Evol. Int. J. Org. Evol. 57: 447–459.
Navarro, A. and Barton, N.H. 2003b. Chromosomal speciation and molecular divergence—Accelerated evolution in rearranged chromosomes. Science 300: 321–324. Olson, M.V. and Varki, A. 2003. Sequencing the chimpanzee genome: Insights into human evolution and disease. Nat. Rev. Genet. 4: 20–28.[CrossRef][Medline] Sadato, N., Pascual-Leone, A., Grafman, J., Ibanez, V., Deiber, M.P., Dold, G., and Hallett, M. 1996. Activation of the primary visual cortex by Braille reading in blind subjects. Nature 380: 526–528.[CrossRef][Medline] Samonte, R.V. and Eichler, E.E. 2002. Segmental duplications and the evolution of the primate genome. Nat. Rev. Genet. 3: 65–72.[Medline]
Sandberg, R., Yasuda, R., Pankratz, D.G., Carter, T.A., Del Rio, J.A., Wodicka, L., Mayford, M., Lockhart, D.J., and Barlow, C. 2000. Regional and strain-specific gene expression mapping in the adult mouse brain. Proc. Natl. Acad. Sci. 97: 11038–11043.
Uddin, M., Wildman, D.E., Liu, G., Xu, W., Johnson, R.M., Hof, P.R., Kapatos, G., Grossman, L.I., and Goodman, M. 2004. Sister grouping of chimpanzees and humans as revealed by genome-wide phylogenetic analysis of brain gene expression profiles. Proc. Natl. Acad. Sci. 101: 2957–2962. von Melchner, L., Pallas, S.L., and Sur, M. 2000. Visual behaviour mediated by retinal projections directed to the auditory pathway. Nature 404: 871–876.[CrossRef][Medline]
Yunis, J.J. and Prakash, O. 1982. The origin of man: A chromosomal pictorial legacy. Science 215: 1525–1530.
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ABSTRACT
RESULTS
0.95 or p 
0.05 and 
-actin genes used as quality controls on Affymetrix microarrays. Labeling of 5 mg of the RNA, hybridization, staining, washing steps, and array scanning were carried out following Affymetrix protocols. 
