메뉴 건너뛰기




Volumn 23, Issue 10, 2007, Pages 1235-1242

Using DNA microarrays to study gene expression in closely related species

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA;

EID: 34447336411     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btm111     Document Type: Article
Times cited : (55)

References (41)
  • 1
    • 33745483813 scopus 로고    scopus 로고
    • Derivation of species-specific hybridization-like knowledge out of cross-species hybridization results
    • Bar-Or,C. et al. (2006) Derivation of species-specific hybridization-like knowledge out of cross-species hybridization results. BMC Genomics, 7, 110.
    • (2006) BMC Genomics , vol.7 , pp. 110
    • Bar-Or, C.1
  • 2
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini,Y. and Hochberg,Y. (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. B, 57, 289-300.
    • (1995) J. R. Stat. Soc. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 3
    • 0034948009 scopus 로고    scopus 로고
    • DNA microarray analysis of chimpanzee liver during acute resolving hepatitis C virus infection
    • Bigger,C.B. et al. (2001) DNA microarray analysis of chimpanzee liver during acute resolving hepatitis C virus infection. J. Virol. 75, 7059-7066.
    • (2001) J. Virol , vol.75 , pp. 7059-7066
    • Bigger, C.B.1
  • 4
    • 7244240339 scopus 로고    scopus 로고
    • Intrahepatic gene expression during chronic hepatitis C virus infection in chimpanzees
    • Bigger,C.B. et al. (2004) Intrahepatic gene expression during chronic hepatitis C virus infection in chimpanzees. J. Virol., 78, 13779-13792.
    • (2004) J. Virol , vol.78 , pp. 13779-13792
    • Bigger, C.B.1
  • 5
    • 0032919458 scopus 로고    scopus 로고
    • Options available-from start to finish-for obtaining expression data by microarray
    • Bowtell,D.D. (1999) Options available-from start to finish-for obtaining expression data by microarray. Nat. Genet., 21, 25-32.
    • (1999) Nat. Genet , vol.21 , pp. 25-32
    • Bowtell, D.D.1
  • 6
    • 0035130163 scopus 로고    scopus 로고
    • Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees
    • 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.
    • (2000) Am. J. Hum. Genet , vol.68 , pp. 444-456
    • Chen, F.C.1    Li, W.H.2
  • 7
    • 24344500211 scopus 로고    scopus 로고
    • Consortium,T.C.S.a.A. (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature, 437, 69-87.
    • Consortium,T.C.S.a.A. (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature, 437, 69-87.
  • 8
    • 1342330572 scopus 로고    scopus 로고
    • A benchmark for affymetrix GeneChip expression measures
    • Cope,L.M. et al. (2004) A benchmark for affymetrix GeneChip expression measures. Bioinformatics, 20, 323-331.
    • (2004) Bioinformatics , vol.20 , pp. 323-331
    • Cope, L.M.1
  • 9
    • 21244474352 scopus 로고    scopus 로고
    • Microarray analysis of selection lines from outbred populations to identify genes involved with nematode parasite resistance in sheep
    • Diez-Tascon,C. et al. (2005) Microarray analysis of selection lines from outbred populations to identify genes involved with nematode parasite resistance in sheep. Physiol. Genomics, 21, 59-69.
    • (2005) Physiol. Genomics , vol.21 , pp. 59-69
    • Diez-Tascon, C.1
  • 10
    • 26444590517 scopus 로고    scopus 로고
    • Construction and validation of a bovine innate immune microarray
    • Donaldson,L. et al. (2005) Construction and validation of a bovine innate immune microarray. BMC Genomics, 6, 135.
    • (2005) BMC Genomics , vol.6 , pp. 135
    • Donaldson, L.1
  • 11
    • 31444431754 scopus 로고    scopus 로고
    • Reliability and reproducibility issues in DNA microarray measurements
    • Draghici,S. et al. (2006) Reliability and reproducibility issues in DNA microarray measurements. Trends Genet, 22, 101-109.
    • (2006) Trends Genet , vol.22 , pp. 101-109
    • Draghici, S.1
  • 12
    • 0033031437 scopus 로고    scopus 로고
    • DNA arrays for analysis of gene expression
    • Eisen,M.B. and Brown,P.O. (1999) DNA arrays for analysis of gene expression. Methods Enzymol., 303, 179-205.
    • (1999) Methods Enzymol , vol.303 , pp. 179-205
    • Eisen, M.B.1    Brown, P.O.2
  • 13
    • 0037066542 scopus 로고    scopus 로고
    • Intra- and interspecific variation in primate gene expression patterns
    • Enard,W. et al. (2002) Intra- and interspecific variation in primate gene expression patterns. Science, 296, 340-343.
    • (2002) Science , vol.296 , pp. 340-343
    • Enard, W.1
  • 14
    • 33750959204 scopus 로고    scopus 로고
    • Using DNA microarrays to study natural variation
    • Gilad,Y. and Borevitz,J. (2006) Using DNA microarrays to study natural variation. Curr. Opin. Genet. Dev., 16, 553-558.
    • (2006) Curr. Opin. Genet. Dev , vol.16 , pp. 553-558
    • Gilad, Y.1    Borevitz, J.2
  • 15
    • 33644855479 scopus 로고    scopus 로고
    • Expression profiling in primates reveals a rapid evolution of human transcription factors
    • Gilad,Y. et al. (2006) Expression profiling in primates reveals a rapid evolution of human transcription factors. Nature, 440, 242-245.
    • (2006) Nature , vol.440 , pp. 242-245
    • Gilad, Y.1
  • 16
    • 19844365733 scopus 로고    scopus 로고
    • Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles
    • Gilad,Y. et al. (2005) Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome. Res., 15, 674-680.
    • (2005) Genome. Res , vol.15 , pp. 674-680
    • Gilad, Y.1
  • 17
    • 4544330058 scopus 로고    scopus 로고
    • Gastric transcription profile of Helicobacter pylori infection in the rhesus macaque
    • Huff,J.L. et al. (2004) Gastric transcription profile of Helicobacter pylori infection in the rhesus macaque. Infect. Immun. 72, 5216-5226.
    • (2004) Infect. Immun , vol.72 , pp. 5216-5226
    • Huff, J.L.1
  • 18
    • 0142121516 scopus 로고    scopus 로고
    • Exploration, normalization, and summaries of high density oligonucleotide array probe level data
    • Irizarry,R.A. et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4, 249-264.
    • (2003) Biostatistics , vol.4 , pp. 249-264
    • Irizarry, R.A.1
  • 19
    • 22144447840 scopus 로고    scopus 로고
    • Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees
    • Khaitovich,P. et al. (2005) Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees. Science, 309, 1850-1854.
    • (2005) Science , vol.309 , pp. 1850-1854
    • Khaitovich, P.1
  • 20
    • 4444287699 scopus 로고    scopus 로고
    • Regional patterns of gene expression in human and chimpanzee brains
    • Khaitovich,P. et al. (2004a) Regional patterns of gene expression in human and chimpanzee brains. Genome. Res., 14, 1462-1473.
    • (2004) Genome. Res , vol.14 , pp. 1462-1473
    • Khaitovich, P.1
  • 21
    • 19344372220 scopus 로고    scopus 로고
    • A neutral model of transcriptome evolution
    • Khaitovich,P. et al. (2004b) A neutral model of transcriptome evolution. PLoS Biol., 2, E132.
    • (2004) PLoS Biol , vol.2
    • Khaitovich, P.1
  • 22
    • 33747607258 scopus 로고    scopus 로고
    • Genetic diversity contribution to errors in short oligonucleotide microarray analysis
    • Kirst,M. et al. (2006) Genetic diversity contribution to errors in short oligonucleotide microarray analysis. Plant Biotechnol. J., 4, 489-498.
    • (2006) Plant Biotechnol. J , vol.4 , pp. 489-498
    • Kirst, M.1
  • 23
    • 33749148061 scopus 로고    scopus 로고
    • Sex-specific expression of alternative transcripts in Drosophila
    • McIntyre,L.M. et al. (2006) Sex-specific expression of alternative transcripts in Drosophila. Genome Biol., 7, R79.
    • (2006) Genome Biol , vol.7
    • McIntyre, L.M.1
  • 24
    • 3042591076 scopus 로고    scopus 로고
    • Common pattern of evolution of gene expression level and protein sequence in Drosophila
    • Nuzhdin,S.V. et al. (2004) Common pattern of evolution of gene expression level and protein sequence in Drosophila. Mol. Biol. Evol. 21, 1308-1317.
    • (2004) Mol. Biol. Evol , vol.21 , pp. 1308-1317
    • Nuzhdin, S.V.1
  • 26
    • 0037504137 scopus 로고    scopus 로고
    • Sex-dependent gene expression and evolution of the Drosophila transcriptome
    • Ranz,J.M. et al. (2003) Sex-dependent gene expression and evolution of the Drosophila transcriptome. Science, 300, 1742-1745.
    • (2003) Science , vol.300 , pp. 1742-1745
    • Ranz, J.M.1
  • 27
    • 0037313182 scopus 로고    scopus 로고
    • Evolution of gene expression in the Drosophila melanogaster subgroup
    • Rifkin,S.A. et al. (2003) Evolution of gene expression in the Drosophila melanogaster subgroup. Nat. Genet., 33, 138-144.
    • (2003) Nat. Genet , vol.33 , pp. 138-144
    • Rifkin, S.A.1
  • 28
    • 3042757551 scopus 로고    scopus 로고
    • From wild wolf to domestic dog: Gene expression changes in the brain
    • Saetre,P. et al. (2004) From wild wolf to domestic dog: Gene expression changes in the brain. Brain Res. Mol. Brain Res., 126, 198-206.
    • (2004) Brain Res. Mol. Brain Res , vol.126 , pp. 198-206
    • Saetre, P.1
  • 29
    • 31544483310 scopus 로고    scopus 로고
    • A new method to remove hybridization bias for interspecies comparison of global gene expression profiles uncovers an association between mRNA sequence divergence and differential gene expression in Xenopus
    • Sartor,M.A. et al. (2006) A new method to remove hybridization bias for interspecies comparison of global gene expression profiles uncovers an association between mRNA sequence divergence and differential gene expression in Xenopus. Nucleic Acids Res., 34 185-200.
    • (2006) Nucleic Acids Res , vol.34 , pp. 185-200
    • Sartor, M.A.1
  • 30
    • 0034088857 scopus 로고    scopus 로고
    • A gene expression database for the molecular pharmacology of cancer
    • Scherf,U. et al. (2000) A gene expression database for the molecular pharmacology of cancer. Nat. Genet., 24, 236-244.
    • (2000) Nat. Genet , vol.24 , pp. 236-244
    • Scherf, U.1
  • 31
    • 1942455815 scopus 로고    scopus 로고
    • Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks
    • Shapiro,M.D. et al. (2004) Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks. Nature, 428, 717-723.
    • (2004) Nature , vol.428 , pp. 717-723
    • Shapiro, M.D.1
  • 32
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical bayes methods for assessing differential expression in microarray experiments
    • Epub Feb, 2012
    • Smyth,G.K. (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol., 3(Epub 2004 Feb 2012).
    • (2004) Stat. Appl. Genet. Mol. Biol , vol.3
    • Smyth, G.K.1
  • 33
    • 33748491517 scopus 로고    scopus 로고
    • The microarray quality control (MAQC) project shows interand intraplatform reproducibility of gene expression measurements
    • Shi,L. et al. (2006) The microarray quality control (MAQC) project shows interand intraplatform reproducibility of gene expression measurements. Nat. Biotechnol., 24, 1151-1161.
    • (2006) Nat. Biotechnol , vol.24 , pp. 1151-1161
    • Shi, L.1
  • 34
    • 33644872577 scopus 로고    scopus 로고
    • Limma: Linear models for microarray data
    • Gentleman,R, Carey,V, Dudoit,S, Irizarry,R. and Huber,W, eds, Springer, New York, pp
    • Smyth,G.K. (2005) Limma: Linear models for microarray data. In Gentleman,R., Carey,V., Dudoit,S., Irizarry,R. and Huber,W. (eds.), Bioinformatics and Computational Biology Solutions using R and Bioconductor. Springer, New York, pp. 397-420.
    • (2005) Bioinformatics and Computational Biology Solutions using R and Bioconductor , pp. 397-420
    • Smyth, G.K.1
  • 35
    • 34447306156 scopus 로고    scopus 로고
    • Smyth,G.K, 2006 statmod: Statistical Modeling. R package version 1.2.4
    • Smyth,G.K. (2006) statmod: Statistical Modeling. R package version 1.2.4.
  • 36
    • 18744369640 scopus 로고    scopus 로고
    • Use of within-array replicate spots for assessing differential expression in microarray experiments
    • Smyth,G.K. et al. (2005) Use of within-array replicate spots for assessing differential expression in microarray experiments. Bioinformatics, 21, 2067-2075.
    • (2005) Bioinformatics , vol.21 , pp. 2067-2075
    • Smyth, G.K.1
  • 37
    • 0037507685 scopus 로고    scopus 로고
    • Patterns of gene expression in peripheral blood mononuclear cells of rhesus macaques infected with SIVmac251 and exhibiting differential rates of disease progression
    • Vahey,M.T. et al. (2003) Patterns of gene expression in peripheral blood mononuclear cells of rhesus macaques infected with SIVmac251 and exhibiting differential rates of disease progression. AIDS Res. Hum. Retroviruses, 19, 369-387.
    • (2003) AIDS Res. Hum. Retroviruses , vol.19 , pp. 369-387
    • Vahey, M.T.1
  • 38
    • 33644778724 scopus 로고    scopus 로고
    • Long versus short oligonucleotide microarrays for the study of gene expression in nonhuman primates
    • Walker,S.J. et al. (2006) Long versus short oligonucleotide microarrays for the study of gene expression in nonhuman primates. J. Neurosci. Methods, 152, 179-189.
    • (2006) J. Neurosci. Methods , vol.152 , pp. 179-189
    • Walker, S.J.1
  • 39
    • 0346101497 scopus 로고    scopus 로고
    • Comparative linkage-disequilibrium analysis of the beta-globin hotspot in primates
    • Wall,J.D. et al. (2003) Comparative linkage-disequilibrium analysis of the beta-globin hotspot in primates. Am. J. Hum. Genet. 73, 1330-1340.
    • (2003) Am. J. Hum. Genet , vol.73 , pp. 1330-1340
    • Wall, J.D.1
  • 40
    • 1342294092 scopus 로고    scopus 로고
    • Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation
    • Yang,Y.H. et al. (2002) Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res., 30, e15.
    • (2002) Nucleic Acids Res , vol.30
    • Yang, Y.H.1
  • 41
    • 4043137829 scopus 로고    scopus 로고
    • Normalization for Two-color cDNA Microarray Data
    • Goldstein,D, ed, Science and Statistics: A Festschrift for Terry Speed. MS
    • Yang,Y.H. and Thorne,N. (2003) Normalization for Two-color cDNA Microarray Data. In Goldstein,D. (ed.), Science and Statistics: A Festschrift for Terry Speed. MS Lecture Notes, Monograph Series, pp. 403-418.
    • (2003) Lecture Notes, Monograph Series , pp. 403-418
    • Yang, Y.H.1    Thorne, N.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.