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Volumn 34, Issue 1, 2006, Pages 185-200

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

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

EID: 31544483310     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkj413     Document Type: Article
Times cited : (37)

References (36)
  • 1
    • 0036896318 scopus 로고    scopus 로고
    • Perspective on the Xenopus field
    • Gurdon,J.B. (2002) Perspective on the Xenopus field. Dev. Dyn., 225, 379.
    • (2002) Dev. Dyn. , vol.225 , pp. 379
    • Gurdon, J.B.1
  • 4
    • 0031853867 scopus 로고    scopus 로고
    • Frog genetics: Xenopus tropicalis jumps into the future
    • Amaya,E., Offield,M.F. and Grainger,R.M. (1998) Frog genetics: Xenopus tropicalis jumps into the future. Trends Genet., 14, 253-255.
    • (1998) Trends Genet , vol.14 , pp. 253-255
    • Amaya, E.1    Offield, M.F.2    Grainger, R.M.3
  • 5
    • 0036895152 scopus 로고    scopus 로고
    • Xenopus, the next generation: X.tropicalis genetics and genomics
    • Hirsch,N., Zimmerman,L.B. and Grainger,R.M. (2002) Xenopus, the next generation: X.tropicalis genetics and genomics. Dev. Dyn., 225, 422-433.
    • (2002) Dev. Dyn. , vol.225 , pp. 422-433
    • Hirsch, N.1    Zimmerman, L.B.2    Grainger, R.M.3
  • 7
    • 0036920815 scopus 로고    scopus 로고
    • Gene profiling during neural induction in Xenopus laevis: Regulation of BMP signaling by post-transcriptional mechanisms and TAB3, a novel TAK1-binding protein
    • Munoz-Sanjuan,I., Bell,E., Altmann,C.R., Vonica,A. and Brivanlou,A.H. (2002) Gene profiling during neural induction in Xenopus laevis: regulation of BMP signaling by post-transcriptional mechanisms and TAB3, a novel TAK1-binding protein. Development, 129, 5529-5540.
    • (2002) Development , vol.129 , pp. 5529-5540
    • Munoz-Sanjuan, I.1    Bell, E.2    Altmann, C.R.3    Vonica, A.4    Brivanlou, A.H.5
  • 10
    • 14844326652 scopus 로고    scopus 로고
    • A Xenopus tropicalis oligonucleotide microarray works across species using RNA from Xenopus laevis
    • Chalmers,A.D., Goldstone,K., Smith,J.C., Gilchrist,M., Amaya,E. and Papalopulu,N. (2005) A Xenopus tropicalis oligonucleotide microarray works across species using RNA from Xenopus laevis. Mech. Dev., 122, 355-363.
    • (2005) Mech. Dev. , vol.122 , pp. 355-363
    • Chalmers, A.D.1    Goldstone, K.2    Smith, J.C.3    Gilchrist, M.4    Amaya, E.5    Papalopulu, N.6
  • 11
    • 3042540826 scopus 로고    scopus 로고
    • Defining a large set of full-length clones from a Xenopus tropicalis EST project
    • Gilchrist,M.J., Zorn,A.M., Voigt,J., Smith,J.C., Papalopulu,N. and Amaya,E. (2004) Defining a large set of full-length clones from a Xenopus tropicalis EST project. Dev. Biol., 271, 498-516.
    • (2004) Dev. Biol. , vol.271 , pp. 498-516
    • Gilchrist, M.J.1    Zorn, A.M.2    Voigt, J.3    Smith, J.C.4    Papalopulu, N.5    Amaya, E.6
  • 14
    • 0346059408 scopus 로고    scopus 로고
    • Expression of genes in the TGF-beta signaling pathway is significantly deregulated in smooth muscle cells from aorta of aryl hydrocarbon receptor knockout mice
    • Guo,J., Sartor,M., Karyala,S., Medvedovic,M., Kann,S., Puga,A., Ryan,P. and Tomlinson,C.R (2004) Expression of genes in the TGF-beta signaling pathway is significantly deregulated in smooth muscle cells from aorta of aryl hydrocarbon receptor knockout mice. Toxicol. Appl. Pharmacol., 194, 79-89.
    • (2004) Toxicol. Appl. Pharmacol. , vol.194 , pp. 79-89
    • Guo, J.1    Sartor, M.2    Karyala, S.3    Medvedovic, M.4    Kann, S.5    Puga, A.6    Ryan, P.7    Tomlinson, C.R.8
  • 15
    • 1942453913 scopus 로고    scopus 로고
    • Different global gene expression profiles in benzo[a]pyrene- and dioxin-treated vascular smooth muscle cells of AHR-knockout and wild-type mice
    • Karyala,S., Guo,J., Sartor,M., Medvedovic,M., Kann,S., Puga,A., Ryan,P. and Tomlinson,C.R. (2004) Different global gene expression profiles in benzo[a]pyrene- and dioxin-treated vascular smooth muscle cells of AHR-knockout and wild-type mice. Cardiovasc Toxicol., 4, 47-73.
    • (2004) Cardiovasc Toxicol. , vol.4 , pp. 47-73
    • Karyala, S.1    Guo, J.2    Sartor, M.3    Medvedovic, M.4    Kann, S.5    Puga, A.6    Ryan, P.7    Tomlinson, C.R.8
  • 18
    • 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. Statist. Soc., B 57, 289-399.
    • (1995) J. R. Statist. Soc. , vol.57 B , pp. 289-399
    • Benjamini, Y.1    Hochberg, Y.2
  • 19
    • 0037433040 scopus 로고    scopus 로고
    • Identifying differentially expressed genes using false discovery rate controlling procedures
    • Reiner,A., Yekutieli,D. and Benjamini,Y. (2003) Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics, 19, 368-375.
    • (2003) Bioinformatics , vol.19 , pp. 368-375
    • Reiner, A.1    Yekutieli, D.2    Benjamini, Y.3
  • 20
    • 0036739286 scopus 로고    scopus 로고
    • Bayesian infinite mixture model based clustering of gene expression profiles
    • Medvedovic,M. and Sivaganesan,S. (2002) Bayesian infinite mixture model based clustering of gene expression profiles. Bioinformatics, 18, 1194-1206.
    • (2002) Bioinformatics , vol.18 , pp. 1194-1206
    • Medvedovic, M.1    Sivaganesan, S.2
  • 21
    • 3042686005 scopus 로고    scopus 로고
    • Bayesian mixture model based clustering of replicated microarray data
    • Medvedovic,M., Yeung,K.Y. and Bumgarner,R.E. (2004) Bayesian mixture model based clustering of replicated microarray data. Bioinformatics, 20, 1222-1232.
    • (2004) Bioinformatics , vol.20 , pp. 1222-1232
    • Medvedovic, M.1    Yeung, K.Y.2    Bumgarner, R.E.3
  • 23
    • 0025259313 scopus 로고
    • Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes
    • Karlin,S. and Altschul,S.F. (1990) Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl Acad. Sci. USA, 87, 2264-2268.
    • (1990) Proc. Natl Acad. Sci. USA , vol.87 , pp. 2264-2268
    • Karlin, S.1    Altschul, S.F.2
  • 29
    • 0027423610 scopus 로고
    • Evolution of duplicate genes in a tetraploid animal, Xenopus laevis
    • Hughes,M.K. and Hughes,A.L. (1993) Evolution of duplicate genes in a tetraploid animal, Xenopus laevis. Mol. Biol. Evol., 10, 1360-1369.
    • (1993) Mol. Biol. Evol. , vol.10 , pp. 1360-1369
    • Hughes, M.K.1    Hughes, A.L.2
  • 30
    • 0036845822 scopus 로고    scopus 로고
    • Splitting pairs: The diverging fates of duplicated genes
    • Prince,V.E. and Pickett,F.B. (2002) Splitting pairs: The diverging fates of duplicated genes. Nature Rev. Genet., 3, 827-837.
    • (2002) Nature Rev. Genet. , vol.3 , pp. 827-837
    • Prince, V.E.1    Pickett, F.B.2
  • 31
    • 19844365733 scopus 로고    scopus 로고
    • Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles
    • Gilad,Y., Rifkin,S.A., Bertone,P., Gerstein,M. and White,K.P. (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    Rifkin, S.A.2    Bertone, P.3    Gerstein, M.4    White, K.P.5
  • 32
    • 0037504137 scopus 로고    scopus 로고
    • Sex-dependent gene expression and evolution of the Drosophila transcriptome
    • 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.
    • (2003) Science , vol.300 , pp. 1742-1745
    • Ranz, J.M.1    Castillo-Davis, C.I.2    Meiklejohn, C.D.3    Hartl, D.L.4
  • 33
    • 25444486428 scopus 로고    scopus 로고
    • In vitroidentification and in silico utilization of interspecies sequence similarities using GeneChip technology
    • Grigoryev,D.N., Ma,S.F., Simon,B.A., Irizarry,R.A., Ye,S.Q. and Garcia,J.G. (2005) In vitroidentification and in silico utilization of interspecies sequence similarities using GeneChip technology. BMC Genomics, 6, 62.
    • (2005) BMC Genomics , vol.6 , pp. 62
    • Grigoryev, D.N.1    Ma, S.F.2    Simon, B.A.3    Irizarry, R.A.4    Ye, S.Q.5    Garcia, J.G.6
  • 35
    • 4544237063 scopus 로고    scopus 로고
    • Cross-species comparison of gene expression between human and porcine tissue, using single microarray platform - Preliminary results
    • Shah,G., Azizian,M., Bruch,D., Mehta,R. and Kittur,D. (2004) Cross-species comparison of gene expression between human and porcine tissue, using single microarray platform - preliminary results. Clin. Transplant, 18 (Suppl 12), 76-80.
    • (2004) Clin. Transplant , vol.18 , Issue.SUPPL. 12 , pp. 76-80
    • Shah, G.1    Azizian, M.2    Bruch, D.3    Mehta, R.4    Kittur, D.5
  • 36
    • 13244267052 scopus 로고    scopus 로고
    • Identification and utilization of inter-species conserved (ISC) probesets on Affymetrix human GeneChip platforms for the optimization of the assessment of expression patterns, in non-human primate (NHP) samples
    • Wang,Z., Lewis,M.G., Nau,M.E., Arnold,A. and Vahey,M.T. (2004) Identification and utilization of inter-species conserved (ISC) probesets on Affymetrix human GeneChip platforms for the optimization of the assessment of expression patterns, in non-human primate (NHP) samples. BMC Bioinformatics, 5, 165.
    • (2004) BMC Bioinformatics , vol.5 , pp. 165
    • Wang, Z.1    Lewis, M.G.2    Nau, M.E.3    Arnold, A.4    Vahey, M.T.5


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