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Volumn 5, Issue 1, 2009, Pages 1-9

Open architecture PCR-based methods for differential gene expression analysis

Author keywords

CDNA RDA; Differential gene expression analysis; MRNA fingerprinting; Open architecture systems; SSH

Indexed keywords

COMPLEMENTARY DNA; DNA; MESSENGER RNA; RNA;

EID: 65949083790     PISSN: 15734129     EISSN: None     Source Type: Journal    
DOI: 10.2174/157341209787314954     Document Type: Review
Times cited : (1)

References (51)
  • 1
    • 0028806048 scopus 로고
    • Quantitative monitoring of gene expression patterns with a complementary DNA microarray
    • Schena, M.; Shalon, D.; Davis, R.W.; Brown, P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science, 1995, 270(5235), 467-70.
    • (1995) Science , vol.270 , Issue.5235 , pp. 467-470
    • Schena, M.1    Shalon, D.2    Davis, R.W.3    Brown, P.O.4
  • 3
    • 0033569516 scopus 로고    scopus 로고
    • Pharmacogenomics: Translating functional genomics into rational therapeutics
    • Evans, W.E.; Relling, M.V. Pharmacogenomics: translating functional genomics into rational therapeutics. Science, 1999, 286(5439), 487-91.
    • (1999) Science , vol.286 , Issue.5439 , pp. 487-491
    • Evans, W.E.1    Relling, M.V.2
  • 4
    • 0032524383 scopus 로고    scopus 로고
    • Wang, D.G.; Fan, J.B.; Siao, C.J.; Berno, A.; Young, P.; Sapolsky, R.; Ghandour, G.; Perkins, N.; Winchester, E.; Spencer, J.; Kruglyak, L.; Stein, L.; Hsie, L.; Topaloglou, T.; Hubbell, E.; Robinson, E.; Mittmann, M.; Morris, M.S.; Shen, N.; Kilburn, D.; Rioux, J.; Nusbaum, C.; Rozen, S.; Hudson, T.J.; Lipshutz, R.; Chee, M.; Lander, E.S. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science, 1998, 280(5366), 1077-82.
    • Wang, D.G.; Fan, J.B.; Siao, C.J.; Berno, A.; Young, P.; Sapolsky, R.; Ghandour, G.; Perkins, N.; Winchester, E.; Spencer, J.; Kruglyak, L.; Stein, L.; Hsie, L.; Topaloglou, T.; Hubbell, E.; Robinson, E.; Mittmann, M.; Morris, M.S.; Shen, N.; Kilburn, D.; Rioux, J.; Nusbaum, C.; Rozen, S.; Hudson, T.J.; Lipshutz, R.; Chee, M.; Lander, E.S. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science, 1998, 280(5366), 1077-82.
  • 9
    • 0026674886 scopus 로고
    • Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction
    • Liang, P.; Pardee, A.B. Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science, 1992, 257(5072), 967-71.
    • (1992) Science , vol.257 , Issue.5072 , pp. 967-971
    • Liang, P.1    Pardee, A.B.2
  • 10
    • 0028220684 scopus 로고
    • Molecular cloning of five messenger RNAs differentially expressed in preneoplastic or neoplastic JB6 mouse epidermal cells: One is homologous to human tissue inhibitor of metalloproteinases-3
    • Sun, Y.; Hegamyer, G.; Colburn, N.H. Molecular cloning of five messenger RNAs differentially expressed in preneoplastic or neoplastic JB6 mouse epidermal cells: one is homologous to human tissue inhibitor of metalloproteinases-3. Cancer Res., 1994, 54(5), 1139-44.
    • (1994) Cancer Res , vol.54 , Issue.5 , pp. 1139-1144
    • Sun, Y.1    Hegamyer, G.2    Colburn, N.H.3
  • 11
    • 0032534541 scopus 로고    scopus 로고
    • Different strategies of differential display: Areas of application
    • Matz, M.V.; Lukyanov, S.A. Different strategies of differential display: areas of application. Nucleic Acids Res., 1998, 26(24), 5537-43.
    • (1998) Nucleic Acids Res , vol.26 , Issue.24 , pp. 5537-5543
    • Matz, M.V.1    Lukyanov, S.A.2
  • 12
    • 0030071742 scopus 로고    scopus 로고
    • Analysis of differential gene expression by display of 3′ end restriction fragments of cDNAs
    • Prashar, Y.; Weissman, S.M. Analysis of differential gene expression by display of 3′ end restriction fragments of cDNAs. Proc. Natl. Acad. Sci. USA, 1996, 93(2), 659-63.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , Issue.2 , pp. 659-663
    • Prashar, Y.1    Weissman, S.M.2
  • 13
    • 0030738232 scopus 로고    scopus 로고
    • Ordered differential display: A simple method for systematic comparison of gene expression profiles
    • Matz, M.; Usman, N.; Shagin, D.; Bogdanova, E.; Lukyanov, S. Ordered differential display: a simple method for systematic comparison of gene expression profiles. Nucleic Acids Res., 1997, 25(12), 2541-42.
    • (1997) Nucleic Acids Res , vol.25 , Issue.12 , pp. 2541-2542
    • Matz, M.1    Usman, N.2    Shagin, D.3    Bogdanova, E.4    Lukyanov, S.5
  • 16
    • 0030138199 scopus 로고    scopus 로고
    • Visualization of differential gene expression using a novel method of RNA fingerprinting based on AFLP: Analysis of gene expression during potato tuber development
    • Bachem, C.W.; van der Hoeven, R.S.; de Bruijn, S.M.; Vreugdenhil, D.; Zabeau, M.; Visser, R.G. Visualization of differential gene expression using a novel method of RNA fingerprinting based on AFLP: analysis of gene expression during potato tuber development. Plant J., 1996, 9(5), 745-53.
    • (1996) Plant J , vol.9 , Issue.5 , pp. 745-753
    • Bachem, C.W.1    van der Hoeven, R.S.2    de Bruijn, S.M.3    Vreugdenhil, D.4    Zabeau, M.5    Visser, R.G.6
  • 17
    • 0018726381 scopus 로고
    • Regulation of a group of abundant mRNA sequences during Friend cell differentiation
    • Affara, N.; Daubas, P. Regulation of a group of abundant mRNA sequences during Friend cell differentiation. Dev. Biol., 1979, 72(1), 110-25.
    • (1979) Dev. Biol , vol.72 , Issue.1 , pp. 110-125
    • Affara, N.1    Daubas, P.2
  • 18
    • 0018932243 scopus 로고
    • Developmental gene regulation in Aspergillus nidulans
    • Timberlake, W.E. Developmental gene regulation in Aspergillus nidulans. Dev. Biol., 1980, 78(2), 497-510.
    • (1980) Dev. Biol , vol.78 , Issue.2 , pp. 497-510
    • Timberlake, W.E.1
  • 19
    • 0027468779 scopus 로고
    • Cloning the differences between two complex genomes
    • Lisitsyn, N.; Lisitsyn, N.; Wigler, M. Cloning the differences between two complex genomes. Science, 1993, 259(5097), 946-51.
    • (1993) Science , vol.259 , Issue.5097 , pp. 946-951
    • Lisitsyn, N.1    Lisitsyn, N.2    Wigler, M.3
  • 20
    • 0028577898 scopus 로고
    • Identifying differences in mRNA expression by representational difference analysis of cDNA
    • Hubank, M.; Schatz, D.G. Identifying differences in mRNA expression by representational difference analysis of cDNA. Nucleic Acids Res., 1994, 22(25), 5640-48.
    • (1994) Nucleic Acids Res , vol.22 , Issue.25 , pp. 5640-5648
    • Hubank, M.1    Schatz, D.G.2
  • 21
    • 0033396516 scopus 로고    scopus 로고
    • Representational difference analysis of cDNA for the detection of differential gene expression in bacteria: Development using a model of iron-regulated gene expression in Neisseria meningitidis
    • Bowler, L.D.; Hubank, M.; Spratt, B.G. Representational difference analysis of cDNA for the detection of differential gene expression in bacteria: development using a model of iron-regulated gene expression in Neisseria meningitidis. Microbiology, 1999, 145(Pt 12), 3529-37.
    • (1999) Microbiology , vol.145 , Issue.PART 12 , pp. 3529-3537
    • Bowler, L.D.1    Hubank, M.2    Spratt, B.G.3
  • 22
    • 0030855424 scopus 로고    scopus 로고
    • Isolation of rare transcripts by representational difference analysis
    • O'Neill, M.J.; Sinclair, A.H. Isolation of rare transcripts by representational difference analysis. Nucleic Acids Res., 1997, 25(13), 2681-82.
    • (1997) Nucleic Acids Res , vol.25 , Issue.13 , pp. 2681-2682
    • O'Neill, M.J.1    Sinclair, A.H.2
  • 23
    • 0034661973 scopus 로고    scopus 로고
    • Optimization of cDNA representational difference analysis for the identification of differentially expressed mRNAs
    • Pastorian, K; Hawel, L 3rd; Byus, C.V. Optimization of cDNA representational difference analysis for the identification of differentially expressed mRNAs. Anal. Biochem., 2000, 283(1), 89-98.
    • (2000) Anal. Biochem , vol.283 , Issue.1 , pp. 89-98
    • Pastorian, K.1    Hawel 3rd, L.2    Byus, C.V.3
  • 24
    • 11144304497 scopus 로고    scopus 로고
    • Modified representational difference analysis: Isolation of differentially expressed mRNAs from rare cell populations
    • O'Hara, E.F.; Williams, M.B.; Rott, L.; Abola, P.; Hansen, N.; Jones, T.; Gurjal, M.R.; Federspiel, N.; Butcher, E.C. Modified representational difference analysis: isolation of differentially expressed mRNAs from rare cell populations. Anal. Biochem., 2005, 336(2), 221-30.
    • (2005) Anal. Biochem , vol.336 , Issue.2 , pp. 221-230
    • O'Hara, E.F.1    Williams, M.B.2    Rott, L.3    Abola, P.4    Hansen, N.5    Jones, T.6    Gurjal, M.R.7    Federspiel, N.8    Butcher, E.C.9
  • 25
    • 0141794164 scopus 로고    scopus 로고
    • Selectively primed adaptive driver RDA (SPAD-RDA): An improved method for subtractive hybridization
    • Birkenmeyer, L.G.; Leary, T.P.; Muerhoff, A.S.; Dawson, G.J.; Mushahwar, I.K.; Desai, S.M. Selectively primed adaptive driver RDA (SPAD-RDA): an improved method for subtractive hybridization. J. Med. Virol., 2003, 71(1), 150-59.
    • (2003) J. Med. Virol , vol.71 , Issue.1 , pp. 150-159
    • Birkenmeyer, L.G.1    Leary, T.P.2    Muerhoff, A.S.3    Dawson, G.J.4    Mushahwar, I.K.5    Desai, S.M.6
  • 28
    • 27144541801 scopus 로고    scopus 로고
    • A novel transcriptome subtraction method for the detection of differentially expressed genes in highly complex eukaryotes
    • Li, L.; Techel, D.; Gretz, N.; Hildebrandt, A. A novel transcriptome subtraction method for the detection of differentially expressed genes in highly complex eukaryotes. Nucleic Acids Res., 2005, 33(16), e136.
    • (2005) Nucleic Acids Res , vol.33 , Issue.16
    • Li, L.1    Techel, D.2    Gretz, N.3    Hildebrandt, A.4
  • 31
    • 36148966169 scopus 로고    scopus 로고
    • Kamchatka crab duplex-specific nuclease-mediated transcriptome subtraction method for identifying long cDNAs of differentially expressed genes
    • Peng, R.H.; Xiong, A.S.; Xue, Y.; Li, X.; Liu, J.G.; Cai, B.; Yao, Q.H. Kamchatka crab duplex-specific nuclease-mediated transcriptome subtraction method for identifying long cDNAs of differentially expressed genes. Anal. Biochem., 2008, 372(2), 148-55.
    • (2008) Anal. Biochem , vol.372 , Issue.2 , pp. 148-155
    • Peng, R.H.1    Xiong, A.S.2    Xue, Y.3    Li, X.4    Liu, J.G.5    Cai, B.6    Yao, Q.H.7
  • 32
    • 0031010405 scopus 로고    scopus 로고
    • Selective amplification via biotin- and restriction-mediated enrichment (SABRE), a novel selective amplification procedure for detection of differentially expressed mRNAs
    • Lavery, D.J.; Lopez-Molina, L.; Fleury-Olela, F.; Schibler, U. Selective amplification via biotin- and restriction-mediated enrichment (SABRE), a novel selective amplification procedure for detection of differentially expressed mRNAs. Proc. Natl. Acad. Sci. USA, 1997, 94(13), 6831-36.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , Issue.13 , pp. 6831-6836
    • Lavery, D.J.1    Lopez-Molina, L.2    Fleury-Olela, F.3    Schibler, U.4
  • 33
    • 0035377585 scopus 로고    scopus 로고
    • Analysis of circadian liver gene expression by ADDER, a highly sensitive method for the display of differentially expressed mRNAs
    • Kornmann, B.; Preitner, N.; Rifat, D.; Fleury-Olela, F.; Schibler, U. Analysis of circadian liver gene expression by ADDER, a highly sensitive method for the display of differentially expressed mRNAs. Nucleic Acids Res., 2001, 29(11), E51-1.
    • (2001) Nucleic Acids Res , vol.29 , Issue.11
    • Kornmann, B.1    Preitner, N.2    Rifat, D.3    Fleury-Olela, F.4    Schibler, U.5
  • 34
    • 33745310918 scopus 로고    scopus 로고
    • Primer Extension Enrichment Reaction (PEER): A new subtraction method for identification of genetic differences between biological specimens
    • Ganova-Raeva, L.; Zhang, X.; Cao, F.; Fields, H.; Khudyakov, Y. Primer Extension Enrichment Reaction (PEER): a new subtraction method for identification of genetic differences between biological specimens. Nucleic Acids Res., 2006, 34(11), e76.
    • (2006) Nucleic Acids Res , vol.34 , Issue.11
    • Ganova-Raeva, L.1    Zhang, X.2    Cao, F.3    Fields, H.4    Khudyakov, Y.5
  • 35
    • 0032526318 scopus 로고    scopus 로고
    • Detection of differentially expressed genes in primary tumor tissues using representational differences analysis coupled to microarray hybridization
    • Welford, S.M.; Gregg, J.; Chen, E.; Garrison, D.; Sorensen, P.H.; Denny, C.T.; Nelson, S.F. Detection of differentially expressed genes in primary tumor tissues using representational differences analysis coupled to microarray hybridization. Nucleic Acids Res., 1998, 26(12), 3059-65.
    • (1998) Nucleic Acids Res , vol.26 , Issue.12 , pp. 3059-3065
    • Welford, S.M.1    Gregg, J.2    Chen, E.3    Garrison, D.4    Sorensen, P.H.5    Denny, C.T.6    Nelson, S.F.7
  • 36
    • 0033559117 scopus 로고    scopus 로고
    • Combining SSH and cDNA microarrays for rapid identification of differentially expressed genes
    • Yang, G.P.; Ross, D.T.; Kuang, W.W.; Brown, P.O.; Weigel, R.J. Combining SSH and cDNA microarrays for rapid identification of differentially expressed genes. Nucleic Acids Res., 1999, 27(6), 1517-23.
    • (1999) Nucleic Acids Res , vol.27 , Issue.6 , pp. 1517-1523
    • Yang, G.P.1    Ross, D.T.2    Kuang, W.W.3    Brown, P.O.4    Weigel, R.J.5
  • 37
    • 11144252246 scopus 로고    scopus 로고
    • Validation of RNA arbitrarily primed PCR probes hybridized to glass cDNA microarrays: Application to the analysis of limited samples
    • Grau, M.; Solé, X.; Obrador, A.; Tarafa, G.; Vendrell, E.; Valls, J.; Moreno, V.; Peinado, M.A.; Capellá, G. Validation of RNA arbitrarily primed PCR probes hybridized to glass cDNA microarrays: application to the analysis of limited samples. Clin. Chem., 2005, 51(1), 93-101.
    • (2005) Clin. Chem , vol.51 , Issue.1 , pp. 93-101
    • Grau, M.1    Solé, X.2    Obrador, A.3    Tarafa, G.4    Vendrell, E.5    Valls, J.6    Moreno, V.7    Peinado, M.A.8    Capellá, G.9
  • 39
    • 0028041101 scopus 로고
    • Fluorescent differential display: Arbitrarily primed RT-PCR fingerprinting on an automated DNA sequencer
    • Ito, T.; Kito, K.; Adati, N.; Mitsui, Y.; Hagiwara, H.; Sakaki, Y. Fluorescent differential display: arbitrarily primed RT-PCR fingerprinting on an automated DNA sequencer. FEBS Lett., 1994, 351(2), 231-36.
    • (1994) FEBS Lett , vol.351 , Issue.2 , pp. 231-236
    • Ito, T.1    Kito, K.2    Adati, N.3    Mitsui, Y.4    Hagiwara, H.5    Sakaki, Y.6
  • 41
    • 0031670594 scopus 로고    scopus 로고
    • Fluorescent amplified-fragment length polymorphism analysis of an outbreak of group A streptococcal invasive disease
    • Desai, M.; Tanna, A.; Wall, R.; Efstratiou, A.; George, R.; Stanley, J. Fluorescent amplified-fragment length polymorphism analysis of an outbreak of group A streptococcal invasive disease. J. Clin. Microbiol., 1998, 36(11), 3133-37.
    • (1998) J. Clin. Microbiol , vol.36 , Issue.11 , pp. 3133-3137
    • Desai, M.1    Tanna, A.2    Wall, R.3    Efstratiou, A.4    George, R.5    Stanley, J.6
  • 42
    • 0035131547 scopus 로고    scopus 로고
    • High-throughput AFLP analysis using infrared dye-labeled primers and an automated DNA sequencer
    • Myburg, A.A.; Remington, D.L.; O'Malley, D.M.; Sederoff, R.R.; Whetten, R.W. High-throughput AFLP analysis using infrared dye-labeled primers and an automated DNA sequencer. Biotechniques, 2001, 30(2), 348-57.
    • (2001) Biotechniques , vol.30 , Issue.2 , pp. 348-357
    • Myburg, A.A.1    Remington, D.L.2    O'Malley, D.M.3    Sederoff, R.R.4    Whetten, R.W.5
  • 43
    • 0030219962 scopus 로고    scopus 로고
    • mRNA differential display: Application in the discovery of novel pharmacological targets
    • Wang, X.; Ruffolo, R.R. Jr.; Feuerstein, G.Z. mRNA differential display: application in the discovery of novel pharmacological targets. Trends Pharmacol. Sci., 1996, 17(8), 276-9.
    • (1996) Trends Pharmacol. Sci , vol.17 , Issue.8 , pp. 276-279
    • Wang, X.1    Ruffolo Jr., R.R.2    Feuerstein, G.Z.3
  • 44
    • 0035869737 scopus 로고    scopus 로고
    • Modification of representational difference analysis applied to the isolation of forskolin- regulated genes from Schwann cells
    • Bermingham, J.R. Jr.; Shumas, S.; Whisenhunt, T.; Rosenfeld, M.G.; Scherer, S.S. Modification of representational difference analysis applied to the isolation of forskolin- regulated genes from Schwann cells. J. Neurosci. Res., 2001, 63(6), 516-24.
    • (2001) J. Neurosci. Res , vol.63 , Issue.6 , pp. 516-524
    • Bermingham Jr., J.R.1    Shumas, S.2    Whisenhunt, T.3    Rosenfeld, M.G.4    Scherer, S.S.5
  • 45
    • 0035958262 scopus 로고    scopus 로고
    • Monitoring of the subtraction process in solid-phase representational difference analysis: Characterization of a candidate drug
    • Boräng, S.; Andersson, T.; Thelin, A.; Larsson, M.; Odeberg, J.; Lundeberg, J. Monitoring of the subtraction process in solid-phase representational difference analysis: characterization of a candidate drug. Gene, 2001, 271(2), 183-92.
    • (2001) Gene , vol.271 , Issue.2 , pp. 183-192
    • Boräng, S.1    Andersson, T.2    Thelin, A.3    Larsson, M.4    Odeberg, J.5    Lundeberg, J.6
  • 46
    • 1642293891 scopus 로고    scopus 로고
    • Characterization of a gene encoding two isoforms of a mitochondrial protein up-regulated by cyclosporin A in activated T cells
    • Mascarell, L.; Auger, R.; Alcover, A.; Ojcius, D.M.; Jungas, T.; Cadet-Daniel, V.; Kanellopoulos, J.M.; Truffa-Bachi, P. Characterization of a gene encoding two isoforms of a mitochondrial protein up-regulated by cyclosporin A in activated T cells. J. Biol. Chem., 2004, 279(11), 10556-63.
    • (2004) J. Biol. Chem , vol.279 , Issue.11 , pp. 10556-10563
    • Mascarell, L.1    Auger, R.2    Alcover, A.3    Ojcius, D.M.4    Jungas, T.5    Cadet-Daniel, V.6    Kanellopoulos, J.M.7    Truffa-Bachi, P.8
  • 47
    • 33947305274 scopus 로고    scopus 로고
    • Identification of novel dioxin-responsive genes by representational difference analysis
    • Rivera, S.P.; Saarikoski, S.T.; Sun, W.; Hankinson, O. Identification of novel dioxin-responsive genes by representational difference analysis. Xenobiotica, 2007, 37(3), 271-79.
    • (2007) Xenobiotica , vol.37 , Issue.3 , pp. 271-279
    • Rivera, S.P.1    Saarikoski, S.T.2    Sun, W.3    Hankinson, O.4
  • 48
    • 27844606998 scopus 로고    scopus 로고
    • SSH adequacy to preimplantation mammalian development: Scarce specific transcripts cloning despite irregular normalisation
    • Bui, L.C.; Léandri, R.D.; Renard, J.P.; Duranthon, V. SSH adequacy to preimplantation mammalian development: scarce specific transcripts cloning despite irregular normalisation. BMC Genomics, 2005, 6, 155.
    • (2005) BMC Genomics , vol.6 , pp. 155
    • Bui, L.C.1    Léandri, R.D.2    Renard, J.P.3    Duranthon, V.4
  • 50
    • 7044273943 scopus 로고    scopus 로고
    • Suppression subtractive hybridization and expression profiling identifies a unique set of genes overexpressed in non-small-cell lung cancer
    • Petroziello, J.; Yamane, A.; Westendorf, L.; Thompson, M.; McDonagh, C.; Cerveny, C.; Law, C.L.; Wahl, A.; Carter, P. Suppression subtractive hybridization and expression profiling identifies a unique set of genes overexpressed in non-small-cell lung cancer. Oncogene, 2004, 23(46), 7734-45.
    • (2004) Oncogene , vol.23 , Issue.46 , pp. 7734-7745
    • Petroziello, J.1    Yamane, A.2    Westendorf, L.3    Thompson, M.4    McDonagh, C.5    Cerveny, C.6    Law, C.L.7    Wahl, A.8    Carter, P.9
  • 51
    • 44449130834 scopus 로고    scopus 로고
    • Killin is a p53-regulated nuclear inhibitor of DNA synthesis
    • Cho, Y.J.; Liang, P. Killin is a p53-regulated nuclear inhibitor of DNA synthesis. Proc. Natl. Acad. Sci. USA, 2008, 105(14), 5396-401.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , Issue.14 , pp. 5396-5401
    • Cho, Y.J.1    Liang, P.2


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