Conservation of regional gene expression in mouse and human brain

PLoS Genetics

Volumn 3, Issue 4, 2007, Pages 0572-0583

  Strand, Andrew D ^a   Aragaki, Aaron K ^a   Baquet, Zachary C ^b   Hodges, Angela ^c   Cunningham, Philip ^c   Holmans, Peter ^d   Jones, Kevin R ^b   Jones, Lesley ^d   Kooperberg, Charles ^a   Olson, James M ^a  

^a Fred Hutchinson Cancer Research Center   (United States)

^b UNIVERSITY OF COLORADO   (United States)

^c KING'S COLLEGE LONDON   (United Kingdom)

^d CARDIFF UNIVERSITY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL TISSUE; ARTICLE; BRAIN REGION; CAUDATE NUCLEUS; CEREBELLUM; CONTROLLED STUDY; DEGENERATIVE DISEASE; DISEASE MODEL; FEMALE; GENE EXPRESSION; HUMAN; HUMAN TISSUE; HUMAN VERSUS ANIMAL COMPARISON; MALE; MICROARRAY ANALYSIS; MOTOR CORTEX; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; ADULT; AGED; ANIMAL; ANTIBODY SPECIFICITY; BRAIN; C57BL MOUSE; COMPARATIVE STUDY; GENE EXPRESSION PROFILING; GENETIC VARIABILITY; METABOLISM; MIDDLE AGED; MOLECULAR EVOLUTION; TISSUE DISTRIBUTION;

MAMMALIA; MUS;

ADULT; AGED; ANIMALS; BRAIN; CONSERVED SEQUENCE; EVOLUTION, MOLECULAR; FEMALE; GENE EXPRESSION; GENE EXPRESSION PROFILING; HUMANS; MALE; MICE; MICE, INBRED C57BL; MIDDLE AGED; ORGAN SPECIFICITY; TISSUE DISTRIBUTION; VARIATION (GENETICS);

EID: 34247554428     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.0030059     Document Type: Article

References (27)

1. Varki A, Altheide TK (2005) Comparing the human and chimpanzee genomes: Searching for needles in a haystack. Genome Res 15: 1746-1758.
2. King MC, Wilson AC (1975) Evolution at two levels in humans and chimpanzees. Science 188: 107-116.
3. Enard W, Khaitovich P, Klose J, Zollner S, Heissig F, et al. (2002) Intra- and inter-specific variation in primate gene expression patterns. Science 296: 340-343.
4. Caceres M, Lachuer J, Zapala MA, Redmond JC, Kudo L, et al. (2003) Elevated gene expression levels distinguish human from non-human primate brains. Proc Natl Acad Sci U S A 100: 13030-13035.
5. Khaitovich P, Muetzel B, She X, Lachmann M, Hellmann I, et al. (2004) Regional patterns of gene expression in human and chimpanzee brains. Genome Res 14: 1462-1473.
6. Gu J, Gu X (2003) Induced gene expression in human brain after the split from chimpanzee. Trends Genet 19: 63-65.
7. Uddin M, Wildman DE, Liu G, Xu W, Johnson RM, et al. (2004) Sister grouping of chimpanzees and humans as revealed by genome-wide phylogenetic analysis of brain gene expression profiles. Proc Natl Acad Sci U S A 101: 2957-2962.
8. Hsieh WP, Chu TM, Wolfinger RD, Gibson G (2003) Mixed-models reanalysis of primate data suggests tissue and species biases in oligonucleotide-based gene expression profiles. Genetics 165: 747-757.
9. Gilad Y, Oshlack A, Smyth GK, Speed TP, White KP (2006) Expression profiling in primates reveals a rapid evolution of human transcription factors. Nature 440: 242-245.
10. Liao BY, Zhang J (2006) Evolutionary conservation of expression profiles between human and mouse orthologous genes. Mol Biol Evol 23: 530-540.
11. Hodges A, Strand AD, Aragaki AK, Kuhn A, Sengstag T, et al. (2005) Regional and cellular gene expression changes in human Huntington's disease brain. Hum Mol Genet 15: 965-977.
12. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264.
13. Smyth GK (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3: Article 3.
14. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, et al. (2004) Bioconductor: Open software development for computational biology and bioinformatics. Genome Biology 5: R80.
15. Jones L, Goldstein DR, Hughes G, Strand AD, Collin F, et al. (2006) Assessment of the relationship between pre-chip and post-chip quality measures for Affymetrix GeneChip expression data. BMC Bioinformatics. 7: 211.
16. Desplats PA, Kass KE, Gilmartin T, Stanwood GD, Woodward EL, et al. (2006) Selective deficits in the expression of striatal-enriched mRNAs in Huntington's disease. J Neurochem 96: 743-757.
17. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: Tool for the unification of biology. Nat Genet 25: 25-29.
18. Braitenberg V, Schuz A (1998) Cortex: Statistics and geometry of neuronal connectivity. 2nd edition. Berlin and New York: Springer Verlag. 249 p.
19. Shepherd GM, Koch C (1998) Introduction to synaptic circuits. In: Shepherd GM, editor. The synaptic organization of the brain. 4th edition. New York: Oxford University Press. 638 p.
20. Kennerly E, Thomson S, Olby N, Breen M, Gibson G (2004) Comparison of regional gene expression differences in the brains of the domestic dog and human. Hum Genomics 1: 435-443.
21. Elo LL, Lahti L, Skottman H, Kylaniemi M, Lahesmaa R, et al. (2005) Integrating probe-level expression changes across generations of Affymetrix arrays. Nucleic Acids Res 33: e193.
22. Khaitovich P, Hellmann I, Enard W, Nowick K, Leinweber M, et al. (2005) Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees. Science 309: 1850-1854.
23. Ahmad-Annuar A, Tabrizi SJ, Fisher EMC (2003) Mouse models as a tool for understanding neurodegenerative diseases. Curr Opin Neurol 16: 451-458.
24. Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, et al. (2000) Functional discovery via a compendium of expression profiles. Cell 102: 109-126.
25. Ward JH (1963) Hierarchical grouping to optimize an objective function. J Am Statist Assoc 58: 236-244.
26. Yang Z (1997) PAML: A program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13: 555-556.
27. Goldman N, Yang Z (1994) A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol 11: 725-736.