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Volumn 2010, Issue 4, 2010, Pages 61-73

Do DNA microarrays tell the story of gene expression?

Author keywords

Burstiness; Clinical applications; DNA microarrays; Gene activity; Genetic regulatory networks; mRNA abundance; Post transcriptional mRNA stability; Reproducibility; Stochasticity; Transcription rate

Indexed keywords

MESSENGER RNA;

EID: 77955499364     PISSN: None     EISSN: 11776250     Source Type: Journal    
DOI: 10.4137/grsb.s4657     Document Type: Article
Times cited : (10)

References (58)
  • 1
    • 77955481403 scopus 로고    scopus 로고
    • Stochastic Oscillations in Genetic Regulatory Networks. Applications to Microarray Experiment, COMPSTAT- 2006
    • in: Rizzi A, Vichi M Edtiors
    • Rosenfeld S. Stochastic Oscillations in Genetic Regulatory Networks. Applications to Microarray Experiment, in: Rizzi A, Vichi M Edtiors. COMPSTAT- 2006. Physica-Verlag. 2006; p. 1609-18.
    • (2006) Physica-Verlag , pp. 1609-1618
    • Rosenfeld, S.1
  • 4
    • 84944263050 scopus 로고    scopus 로고
    • Making the most of microarrays
    • Editorial
    • Editorial, Making the most of microarrays. Nature Biotechnology. 2006; 24:1039.
    • (2006) Nature Biotechnology , vol.24 , pp. 1039
  • 5
    • 33748491517 scopus 로고    scopus 로고
    • The MicroArray Quality Control (MAQC) project shows interand intraplatform reproducibility of gene expression measurements
    • Shi L, et al. The MicroArray Quality Control (MAQC) project shows interand intraplatform reproducibility of gene expression measurements. Nature Biotechnology. 2006;24:1151.
    • (2006) Nature Biotechnology , vol.24 , pp. 1151
    • Shi, L.1
  • 6
    • 8444246272 scopus 로고    scopus 로고
    • QA/QC: Challenges and pitfalls facing the microarray community and regulatory agencies
    • Shi L, et al. QA/QC: challenges and pitfalls facing the microarray community and regulatory agencies. Expert Rev Mol Diagn. 2004;4:761.
    • (2004) Expert Rev Mol Diagn , vol.4 , pp. 761
    • Shi, L.1
  • 7
    • 13444304216 scopus 로고    scopus 로고
    • Microarrays and molecular research: Noise discovery?
    • Ioannidis JP. Microarrays and molecular research: noise discovery? Lancet. 2005;365:454.
    • (2005) Lancet , vol.365 , pp. 454
    • Ioannidis, J.P.1
  • 8
    • 13844308671 scopus 로고    scopus 로고
    • Gene-expression profiling in breast cancer
    • Jenssen TK, Hovig E. Gene-expression profiling in breast cancer. Lancet. 2005;365:634.
    • (2005) Lancet , vol.365 , pp. 634
    • Jenssen, T.K.1    Hovig, E.2
  • 10
    • 0038697629 scopus 로고    scopus 로고
    • The interplay of nuclear mRNP assembly, mRNA surveillance and export
    • Stutz F, Izaurralde E. The interplay of nuclear mRNP assembly, mRNA surveillance and export. Trends Cell Biol. 2003;13:319.
    • (2003) Trends Cell Biol , vol.13 , pp. 319
    • Stutz, F.1    Izaurralde, E.2
  • 11
    • 77955483551 scopus 로고    scopus 로고
    • Characteristics of transcriptional activity in nonlinear dynamics of genetic regulatory networks
    • Rosenfeld S. Characteristics of transcriptional activity in nonlinear dynamics of genetic regulatory networks. Gene Regul Syst Bio. 2009; 3:159.
    • (2009) Gene Regul Syst Bio , vol.3 , pp. 159
    • Rosenfeld, S.1
  • 13
    • 25144492110 scopus 로고    scopus 로고
    • Approximative kinetic formats used in metabolic network modeling
    • Heijnen JJ. Approximative kinetic formats used in metabolic network modeling. Biotechnol Bioeng. 2005;91:534.
    • (2005) Biotechnol Bioeng , vol.91 , pp. 534
    • Heijnen, J.J.1
  • 14
    • 84876731888 scopus 로고    scopus 로고
    • Computational Models of Metabolism: Stability and Regulation in Metabolic Networks
    • in press
    • Steuer R, Junker B. Computational Models of Metabolism: Stability and Regulation in Metabolic Networks, Advances of Chemical Physics (in press) (2009).
    • (2009) Advances of Chemical Physics
    • Steuer, R.1    Junker, B.2
  • 15
    • 65249141709 scopus 로고    scopus 로고
    • Database for mRNA half-life of 19,977 genes obtained by DNA microarray analysis of pluripotent and differentiating mouse embryonic stem cells
    • Sharova LV, et al. Database for mRNA half-life of 19,977 genes obtained by DNA microarray analysis of pluripotent and differentiating mouse embryonic stem cells. DNA Res. 2009;16:45.
    • (2009) DNA Res , vol.16 , pp. 45
    • Sharova, L.V.1
  • 16
    • 0037197892 scopus 로고    scopus 로고
    • Precision and functional specificity in mRNA decay
    • Wang Y, et al. Precision and functional specificity in mRNA decay. Proc Natl Acad Sci U S A. 2002;99:5860.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 5860
    • Wang, Y.1
  • 17
    • 0042330135 scopus 로고    scopus 로고
    • Genome-wide survey of mRNA halflives in Bacillus subtilis identifies extremely stable mRNAs
    • Hambraeus G, von WC, Hederstedt L. Genome-wide survey of mRNA halflives in Bacillus subtilis identifies extremely stable mRNAs. Mol Genet Genomics. 2003;269:706.
    • (2003) Mol Genet Genomics , vol.269 , pp. 706
    • Hambraeus, G.1    Von, W.C.2    Hederstedt, L.3
  • 18
    • 0037115826 scopus 로고    scopus 로고
    • Genome-wide analysis of mRNA decay in resting and activated primary human T lymphocytes
    • Raghavan A, et al. Genome-wide analysis of mRNA decay in resting and activated primary human T lymphocytes. Nucleic Acids Res. 2002;30:5529.
    • (2002) Nucleic Acids Res , vol.30 , pp. 5529
    • Raghavan, A.1
  • 19
    • 4644288309 scopus 로고    scopus 로고
    • Microarray-based analyses of mRNA decay in the regulation of mammalian gene expression
    • Raghavan A, Bohjanen PR. Microarray-based analyses of mRNA decay in the regulation of mammalian gene expression. Brief Funct Genomic Proteomic. 2004;3:112.
    • (2004) Brief Funct Genomic Proteomic , vol.3 , pp. 112
    • Raghavan, A.1    Bohjanen, P.R.2
  • 20
    • 0025952599 scopus 로고
    • A comparison of apparent mRNA half-life using kinetic labeling techniques vs. decay following administration of transcriptional inhibitors
    • Harrold S, Genovese C, Kobrin B, Morrison SL, Milcarek C. A comparison of apparent mRNA half-life using kinetic labeling techniques vs. decay following administration of transcriptional inhibitors. Anal Biochem. 1991;198:19.
    • (1991) Anal Biochem , vol.198 , pp. 19
    • Harrold, S.1    Genovese, C.2    Kobrin, B.3    Morrison, S.L.4    Milcarek, C.5
  • 21
    • 3242726930 scopus 로고    scopus 로고
    • Genomic run-on evaluates transcription rates for all yeast genes and identifies gene regulatory mechanisms
    • Garcia-Martinez J, Aranda A, Perez-Ortin JE. Genomic run-on evaluates transcription rates for all yeast genes and identifies gene regulatory mechanisms. Mol Cell. 2004;15:303.
    • (2004) Mol Cell , vol.15 , pp. 303
    • Garcia-Martinez, J.1    Aranda, A.2    Perez-Ortin, J.E.3
  • 23
    • 35348898041 scopus 로고    scopus 로고
    • Stochastic cooperativity in non-linear dynamics of genetic regulatory networks
    • Rosenfeld S. Stochastic cooperativity in non-linear dynamics of genetic regulatory networks. Math Biosci. 2007;210:121.
    • (2007) Math Biosci , vol.210 , pp. 121
    • Rosenfeld, S.1
  • 25
    • 0027499733 scopus 로고
    • Soluble proteins: Size, shape and function
    • Goodsell DS, Olson AJ. Soluble proteins: size, shape and function. Trends Biochem Sci. 1993;18:65.
    • (1993) Trends Biochem Sci , vol.18 , pp. 65
    • Goodsell, D.S.1    Olson, A.J.2
  • 26
    • 0033779678 scopus 로고    scopus 로고
    • Diffusional protein transport within the nucleus: A message in the medium
    • Pederson T. Diffusional protein transport within the nucleus: a message in the medium. Nat Cell Biol. 2000;2:E73.
    • (2000) Nat Cell Biol , vol.2
    • Pederson, T.1
  • 27
    • 33746649820 scopus 로고    scopus 로고
    • Single molecule measurements of repressor protein 1D diffusion on DNA
    • Wang YM, Austin RH, Cox EC. Single molecule measurements of repressor protein 1D diffusion on DNA. Phys Rev Lett. 2006;97:048302.
    • (2006) Phys Rev Lett , vol.97 , pp. 048302
    • Wang, Y.M.1    Austin, R.H.2    Cox, E.C.3
  • 28
    • 0036204260 scopus 로고    scopus 로고
    • Protein-water interactions
    • Parsegian VA. Protein-water interactions. Int Rev Cytol. 2002;215:1.
    • (2002) Int Rev Cytol , vol.215 , pp. 1
    • Parsegian, V.A.1
  • 29
    • 0035478585 scopus 로고    scopus 로고
    • Macromolecular crowding: Obvious but underappreciated
    • Ellis RJ. Macromolecular crowding: obvious but underappreciated. Trends Biochem Sci. 2001;26:597.
    • (2001) Trends Biochem Sci , vol.26 , pp. 597
    • Ellis, R.J.1
  • 30
    • 35348918883 scopus 로고    scopus 로고
    • Stochastic Simulation of Chemical Kinetics
    • Gillespie DT. Stochastic Simulation of Chemical Kinetics. Annu Rev Phys Chem. 2006.
    • (2006) Annu Rev Phys Chem
    • Gillespie, D.T.1
  • 31
    • 0842265974 scopus 로고    scopus 로고
    • Regulation of RNA polymerase II transcription by sequencespecific DNA binding factors
    • Kadonaga JT. Regulation of RNA polymerase II transcription by sequencespecific DNA binding factors. Cell. 2004;116:247.
    • (2004) Cell , vol.116 , pp. 247
    • Kadonaga, J.T.1
  • 32
    • 77953409526 scopus 로고    scopus 로고
    • Patterns of stochastic behavior in dynamically unstable highdimensional biochemical networks
    • Rosenfeld S. Patterns of stochastic behavior in dynamically unstable highdimensional biochemical networks. Gene Regul Syst Bio. 2009;3:1.
    • (2009) Gene Regul Syst Bio , vol.3 , pp. 1
    • Rosenfeld, S.1
  • 33
    • 33645027986 scopus 로고    scopus 로고
    • Stochastic protein expression in individual cells at the single molecule level
    • Cai L, Friedman N, Xie XS. Stochastic protein expression in individual cells at the single molecule level. Nature. 2006;440:358.
    • (2006) Nature , vol.440 , pp. 358
    • Cai, L.1    Friedman, N.2    Xie, X.S.3
  • 35
    • 0032167516 scopus 로고    scopus 로고
    • Transcription occurs in pulses in muscle fibers
    • Newlands S, et al. Transcription occurs in pulses in muscle fibers. Genes Dev. 1998;12:2748.
    • (1998) Genes Dev , vol.12 , pp. 2748
    • Newlands, S.1
  • 36
    • 0028328719 scopus 로고
    • Transcription of individual genes in eukaryotic cells occurs randomly and infrequently
    • Ross IL, Browne CM, Hume DA. Transcription of individual genes in eukaryotic cells occurs randomly and infrequently, Immunol. Cell Biol. 1994;72:177.
    • (1994) Immunol. Cell Biol , vol.72 , pp. 177
    • Ross, I.L.1    Browne, C.M.2    Hume, D.A.3
  • 38
    • 3843126332 scopus 로고    scopus 로고
    • RNA dynamics in live Escherichia coli cells
    • Golding I, Cox EC. RNA dynamics in live Escherichia coli cells. Proc Natl Acad Sci U S A. 2004;101:11310.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 11310
    • Golding, I.1    Cox, E.C.2
  • 39
    • 28944434119 scopus 로고    scopus 로고
    • Real-time kinetics of gene activity in individual bacteria
    • Golding I, Paulsson J, Zawilski SM, Cox EC. Real-time kinetics of gene activity in individual bacteria. Cell. 2005;123:1025.
    • (2005) Cell , vol.123 , pp. 1025
    • Golding, I.1    Paulsson, J.2    Zawilski, S.M.3    Cox, E.C.4
  • 40
    • 33645033645 scopus 로고    scopus 로고
    • Probing gene expression in live cells, one protein molecule at a time
    • Yu J, Xiao J, Ren X, Lao K, Xie XS. Probing gene expression in live cells, one protein molecule at a time. Science. 2006;311:1600.
    • (2006) Science , vol.311 , pp. 1600
    • Yu, J.1    Xiao, J.2    Ren, X.3    Lao, K.4    Xie, X.S.5
  • 42
    • 0033083733 scopus 로고    scopus 로고
    • It's a noisy business! Genetic regulation at the nanomolar scale
    • McAdams HH, Arkin A. It's a noisy business! Genetic regulation at the nanomolar scale. Trends Genet. 1999;15:65.
    • (1999) Trends Genet , vol.15 , pp. 65
    • McAdams, H.H.1    Arkin, A.2
  • 43
    • 19544379881 scopus 로고    scopus 로고
    • Stochasticity in gene expression: From theories to phenotypes
    • Kaern M, Elston TC, Blake WJ, Collins JJ. Stochasticity in gene expression: from theories to phenotypes. Nat Rev Genet. 2005;6:451.
    • (2005) Nat Rev Genet , vol.6 , pp. 451
    • Kaern, M.1    Elston, T.C.2    Blake, W.J.3    Collins, J.J.4
  • 44
    • 0035193294 scopus 로고    scopus 로고
    • Stochasticity in Transcriptional Regulation: Origins, Consequences, and Mathematical Representations
    • Kepler T, Eiston T. Stochasticity in Transcriptional Regulation: Origins, Consequences, and Mathematical Representations. Biophysical Journal. 2001;81:3116.
    • (2001) Biophysical Journal , vol.81 , pp. 3116
    • Kepler, T.1    Eiston, T.2
  • 45
    • 0036729047 scopus 로고    scopus 로고
    • Can a biologist fix a radio?-Or, what I learned while studying apoptosis
    • Lazebnik Y. Can a biologist fix a radio?-Or, what I learned while studying apoptosis. Cancer Cell. 2002;2:179.
    • (2002) Cancer Cell , vol.2 , pp. 179
    • Lazebnik, Y.1
  • 48
    • 77955487010 scopus 로고    scopus 로고
    • Mathematical Description of Biochemical Networks: Instability, stochasticity, evolution
    • in: Thiangliam S Edtior, Oxford University Press
    • Rosenfeld S. Mathematical Description of Biochemical Networks: instability, stochasticity, evolution, in: Thiangliam S Edtior. Systems Biology of Cancer, Oxford University Press, 2009.
    • (2009) Systems Biology of Cancer
    • Rosenfeld, S.1
  • 49
    • 0015514970 scopus 로고
    • Will a large complex system be stable?
    • May RM. Will a large complex system be stable? Nature. 1972;238:413.
    • (1972) Nature , vol.238 , pp. 413
    • May, R.M.1
  • 50
    • 60349119161 scopus 로고    scopus 로고
    • Reaction systems, graph theory and dynamical networks
    • in: Gauges R, Kummer U, Pahle J, Willy P Editors, University of Heidelberg, Heidelberg
    • Kirkilionis M. Reaction systems, graph theory and dynamical networks, in: Gauges R, Kummer U, Pahle J, Willy P Editors. Fifth Workshop on Computation of Biochemical Pathways and Genetic Networks, University of Heidelberg, Heidelberg, 2008.
    • (2008) Fifth Workshop On Computation of Biochemical Pathways and Genetic Networks
    • Kirkilionis, M.1
  • 51
    • 33745711647 scopus 로고    scopus 로고
    • Estimations of intrinsic and extrinsic noise in models of nonlinear genetic networks
    • Scott M, Ingalls B, Kaern M. Estimations of intrinsic and extrinsic noise in models of nonlinear genetic networks. Chaos. 2006;16:026107.
    • (2006) Chaos , vol.16 , pp. 026107
    • Scott, M.1    Ingalls, B.2    Kaern, M.3
  • 53
    • 0041530047 scopus 로고    scopus 로고
    • Resampling-based Multiple Testing for Microarray Data Analysis
    • Ge Y, Dudoit S, Speed T. Resampling-based Multiple Testing for Microarray Data Analysis. Test. 2003;12:1.
    • (2003) Test , vol.12 , pp. 1
    • Ge, Y.1    Dudoit, S.2    Speed, T.3
  • 54
    • 77955503279 scopus 로고    scopus 로고
    • Detection of Differentially Expressed Genes In Small Sets of cDNA Microarrays
    • Rosenfeld S. Detection of Differentially Expressed Genes In Small Sets of cDNA Microarrays. Journal of Data Science. 2007;5:451.
    • (2007) Journal of Data Science , vol.5 , pp. 451
    • Rosenfeld, S.1
  • 55
    • 74549174585 scopus 로고    scopus 로고
    • DNA microarrays are predictive of cancer prognosis: A reevaluation
    • Fan X, et al. DNA microarrays are predictive of cancer prognosis: a reevaluation. Clin Cancer Res. 2010;16:629.
    • (2010) Clin Cancer Res , vol.16 , pp. 629
    • Fan, X.1
  • 56
    • 33751193656 scopus 로고    scopus 로고
    • Converting a breast cancer microarray signature into a highthroughput diagnostic test
    • Glas AM, et al. Converting a breast cancer microarray signature into a highthroughput diagnostic test. BMC Genomics. 2006;7:278.
    • (2006) BMC Genomics , vol.7 , pp. 278
    • Glas, A.M.1
  • 57
    • 34147164024 scopus 로고    scopus 로고
    • Is molecular profiling ready for use in clinical decision making?
    • Ioannidis JP. Is molecular profiling ready for use in clinical decision making? Oncologist. 2007;12:301.
    • (2007) Oncologist , vol.12 , pp. 301
    • Ioannidis, J.P.1
  • 58
    • 58749109439 scopus 로고    scopus 로고
    • Personalized genetic prediction: Too limited, too expensive, or too soon?
    • Ioannidis JP. Personalized genetic prediction: too limited, too expensive, or too soon? Ann Intern Med. 2009;150:139.
    • (2009) Ann Intern Med , vol.150 , pp. 139
    • Ioannidis, J.P.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.