Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles

Genome Research

Volumn 15, Issue 5, 2005, Pages 674-680

  Gilad, Yoav ^a   Rifkin, Scott A ^a,b   Bertone, Paul ^b   Gerstein, Mark ^b   White, Kevin P ^a,b  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL TISSUE; ARTICLE; CHIMPANZEE; CONTROLLED STUDY; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE SEQUENCE; GENETIC VARIABILITY; HUMAN; HUMAN TISSUE; HYBRIDIZATION; MALE; NONHUMAN; NUCLEOTIDE SEQUENCE; ORANG UTAN; PRIORITY JOURNAL; RHESUS MONKEY; SPECIES COMPARISON; ANIMAL; BIOLOGY; COMPARATIVE STUDY; DNA SEQUENCE; GENETICS; METHODOLOGY; MOLECULAR EVOLUTION; NUCLEIC ACID HYBRIDIZATION; PRIMATE; SPECIES DIFFERENCE; STATISTICAL MODEL;

PAN TROGLODYTES; PONGO PYGMAEUS;

ANIMALS; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENE EXPRESSION PROFILING; HUMANS; LINEAR MODELS; MALE; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PRIMATES; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY;

EID: 19844365733     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.3335705     Document Type: Article

References (38)

1. Andolfatto, P. and Przeworski, M. 2000. A genome-wide departure from the standard neutral model in natural populations of Drosophila. Genetics 156: 257-268.
2. Ascher, D., Dubois, P.F., Hinsen, K., Hugunin, J., and Oliphant, T. 2001. Numerical python. Lawrence Livermore National Laboratory, Livermore, CA.
3. Benjamini, Y. and Hochberg, Y. 1995. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. Royal Stat. Soc. B 57: 289-300.
4. Bolstad, B.M., Irizarry, R.A., Astrand, M., and Speed, T.P. 2003. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193.
5. Bowtell, D.D. 1999. Options available-from start to finish-for obtaining expression data by microarray. Nat. Genet. 21: 25-32.
6. 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.
7. Chen, F.C. and Li, W.H. 2000. Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. Am. J. Hum. Genet. 68: 444-456.
8. Chen, F.C., Vallender, E.J., Wang, H., Tzeng, C.S., and Li, W.H. 2001. Genomic divergence between human and chimpanzee estimated from large-scale alignments of genomic sequences. J. Hered. 92: 481-489.
9. Chen, X., Cheung, S.T., So, S., Fan, S.T., Barry, C., Higgins, J., Lai, K.M., Ji, J., Dudoit, S., Ng, I.O., et al. 2002. Gene expression patterns in human liver cancers. Mol. Biol. Cell 13: 1929-1939.
10. Diehl, F., Grahlmann, S., Beier, M., and Hoheisel, J.D. 2001. Manufacturing DNA microarrays of high spot homogeneity and reduced background signal. Nucleic Acids Res. 29: E38.
11. Ebersberger, I., Metzler, D., Schwarz, C., and Pääbo, S. 2002. Genomewide comparison of DNA sequences between humans and chimpanzees. Am. J. Hum. Genet. 70: 1490-1497.
12. Eisen, M.B. and Brown, P.O. 1999. DNA arrays for analysis of gene expression. Methods Enzymol. 303: 179-205.
13. 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.
14. Fortna, A., Kim, Y., MacLaren, E., Marshall, K., Hahn, G., Meltesen, L., Brenton, M., Hink, R., Burgers, S., Hernandez-Boussard, T., et al. 2004. Lineage-specific gene duplication and loss in human and great ape evolution. PLoS Biol. 2: E207.
15. Gilad, Y., Man, O., Pääbo, S., and Lancet, D. 2003. Human specific loss of olfactory receptor genes. Proc. Natl. Acad. Sci. 100: 3324-3327.
16. Hellmann, I., Zollner, S., Enard, W., Ebersberger, I., Nickel, B., and Pääbo, S. 2003. Selection on human genes as revealed by comparisons to chimpanzee cDNA. Genome Res. 13: 831-837.
17. 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.
18. Kent, W.J. 2002. BLAT-the BLAST-like alignment tool. Genome Res. 12: 656-664.
19. Kerr, M.K., Afshari, C.A., Bennett, L., Bushel, P., Martinez, J., Walker, N.J., and Churchill, G.A. 2002. Statistical analysis of a gene expression microarray experiment with replication. Stat. Sin. 12: 203-217.
20. Khaitovich, P., Weiss, G., Lachmann, M., Hellmann, I., Enard, W., Muetzel, B., Wirkner, U., Ansorge, W., and Pääbo, S. 2004. A neutral model of transcriptome evolution. PLoS Biol. 2: E132.
21. Magwene, P. 2002. disipyl.py-An object-oriented Python interface to DISLIN. http://biology.duke.edu/magwenelab/disipyl.html
22. Meiklejohn, C.D., Parsch, J., Ranz, J.M., and Hartl, D.L. 2003. Rapid evolution of male-biased gene expression in Drosophila. Proc. Natl. Acad. Sci. 100: 9894-9899.
23. Nagpal, S., Karaman, M.W., Timmerman, M.M., Ho, V.V., Pike, B.L., and Hacia, J.G. 2004. Improving the sensitivity and specificity of gene expression analysis in highly related organisms through the use of electronic masks. Nucleic Acids Res. 32: e51.
24. Nuzhdin, S.V., Wayne, M.L., Harmon, K.L., and McIntyre, L.M. 2004. Common pattern of evolution of gene expression level and protein sequence in Drosophila. Mol. Biol. Evol. 21: 1308-1317.
25. Perou, C.M., Sorlie, T., Eisen, M.B., van de Rijn, M., Jeffrey, S.S., Rees, C.A., Pollack, J.R., Ross, D.T., Johnsen, H., Akslen, L.A., et al. 2000. Molecular portraits of human breast tumours. Nature 406: 747-752.
26. Ranz, J.M., Castillo-Davis, C.I., Meiklejohn, C.D., and Hartl, D.L. 2003. Sex-dependent gene expression and evolution of the Drosophila transcriptome. Science 300: 1742-1745.
27. Reinke, V. 2002. Functional exploration of the C. elegans genome using DNA microarrays. Nat. Genet. 32: 541-546.
28. Rifkin, S.A., Kim, J., and White, K.P. 2003. Evolution of gene expression in the Drosophila melanogaster subgroup. Nat. Genet. 33: 138-144.
29. Saetre, P., Lindberg, J., Leonard, J.A., Olsson, K., Pettersson, U., Ellegren, H., Bergstrom, T.F., Vila, C., and Jazin, E. 2004. From wild wolf to domestic dog: Gene expression changes in the brain. Brain Res. Mol. Brain Res. 126: 198-206.
30. Smyth, G.K. and Speed, T. 2003. Normalization of cDNA microarray data. Methods 31: 265-273.
31. Team, R.D.C. 2003. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
32. van Rossum, G. 2003. python. http://www.python.org/.
33. Wall, J.D., Frisse, L.A., Hudson, R.R., and Di Rienzo, A. 2003. Comparative linkage-disequilibrium analysis of the β-globin hotspot in primates. Am. J. Hum. Genet. 73: 1330-1340.
34. White, K.P. 2001. Functional genomics and the study of development, variation and evolution. Nat. Rev. Genet. 2: 528-537.
35. Yang, Y.H., Dudoit, S., Luu, P., and Speed, T.P. 2001. Normalization for cDNA microarray data. In Proceedings of SPIE. Microarrays: Optical technologies and informatics (eds. M.L. Bittner et al.), pp. 141-152. Society for Optical Engineering, San Jose, CA.
36. Yang, Y.H., Dudoit, S., Luu, P., Lin, D.M., Peng, V., Ngai, J., and Speed, T.P. 2002. Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30: e15.
37. http://genome.ucsc.edu/; Human Genome.
38. http://www.ncbi.nlm.nih.gov/RefSeq/; NCBI Sequence Database.