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Volumn 15, Issue 8, 2009, Pages 352-358

Protein-binding microarrays: probing disease markers at the interface of proteomics and genomics

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN; INTERFERON; RIBAVIRIN; TRANSCRIPTION FACTOR;

EID: 68649108381     PISSN: 14714914     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molmed.2009.06.004     Document Type: Article
Times cited : (13)

References (60)
  • 1
    • 0033028741 scopus 로고    scopus 로고
    • Quantifying DNA-protein interactions by double-stranded DNA arrays
    • Bulyk M.L., et al. Quantifying DNA-protein interactions by double-stranded DNA arrays. Nat. Biotechnol. 17 (1999) 573-577
    • (1999) Nat. Biotechnol. , vol.17 , pp. 573-577
    • Bulyk, M.L.1
  • 2
    • 0035912721 scopus 로고    scopus 로고
    • Exploring the DNA-binding specificities of zinc fingers with DNA microarrays
    • Bulyk M.L., et al. Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc. Natl. Acad. Sci. U. S. A. 98 (2001) 7158-7163
    • (2001) Proc. Natl. Acad. Sci. U. S. A. , vol.98 , pp. 7158-7163
    • Bulyk, M.L.1
  • 3
    • 9644268153 scopus 로고    scopus 로고
    • Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays
    • Mukherjee S., et al. Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nat. Genet. 36 (2004) 1331-1339
    • (2004) Nat. Genet. , vol.36 , pp. 1331-1339
    • Mukherjee, S.1
  • 4
    • 27244437971 scopus 로고    scopus 로고
    • Proof of concept for microarray-based detection of DNA-binding oncogenes in cell extracts
    • Egener T., et al. Proof of concept for microarray-based detection of DNA-binding oncogenes in cell extracts. Nucleic Acids Res. 33 (2005) e79
    • (2005) Nucleic Acids Res. , vol.33
    • Egener, T.1
  • 5
    • 32244448130 scopus 로고    scopus 로고
    • Defining the sequence-recognition profile of DNA-binding molecules
    • Warren C.L., et al. Defining the sequence-recognition profile of DNA-binding molecules. Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 867-872
    • (2006) Proc. Natl. Acad. Sci. U. S. A. , vol.103 , pp. 867-872
    • Warren, C.L.1
  • 6
    • 33750882505 scopus 로고    scopus 로고
    • Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities
    • Berger M.F., et al. Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nat. Biotechnol. 24 (2006) 1429-1435
    • (2006) Nat. Biotechnol. , vol.24 , pp. 1429-1435
    • Berger, M.F.1
  • 7
    • 45449115390 scopus 로고    scopus 로고
    • Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences
    • Berger M.F., et al. Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences. Cell 133 (2008) 1266-1276
    • (2008) Cell , vol.133 , pp. 1266-1276
    • Berger, M.F.1
  • 8
    • 51349138269 scopus 로고    scopus 로고
    • Discovery of a hepatitis C target and its pharmacological inhibitors by microfluidic affinity analysis
    • Einav S., et al. Discovery of a hepatitis C target and its pharmacological inhibitors by microfluidic affinity analysis. Nat. Biotechnol. 26 (2008) 1019-1027
    • (2008) Nat. Biotechnol. , vol.26 , pp. 1019-1027
    • Einav, S.1
  • 9
    • 34347256054 scopus 로고    scopus 로고
    • Microfluidic large-scale integration: the evolution of design rules for biological automation
    • Melin J., and Quake S.R. Microfluidic large-scale integration: the evolution of design rules for biological automation. Annu. Rev. Biophys. Biomol. Struct. 36 (2007) 213-231
    • (2007) Annu. Rev. Biophys. Biomol. Struct. , vol.36 , pp. 213-231
    • Melin, J.1    Quake, S.R.2
  • 10
    • 0037131390 scopus 로고    scopus 로고
    • Microfluidic large-scale integration
    • Thorsen T., et al. Microfluidic large-scale integration. Science 298 (2002) 580-584
    • (2002) Science , vol.298 , pp. 580-584
    • Thorsen, T.1
  • 11
    • 2342507824 scopus 로고    scopus 로고
    • Quantitative high-throughput analysis of transcription factor binding specificities
    • Linnell J., et al. Quantitative high-throughput analysis of transcription factor binding specificities. Nucleic Acids Res. 32 (2004) e44
    • (2004) Nucleic Acids Res. , vol.32
    • Linnell, J.1
  • 12
    • 0037174671 scopus 로고    scopus 로고
    • Transcriptional regulatory networks in Saccharomyces cerevisiae
    • Lee T.I., et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298 (2002) 799-804
    • (2002) Science , vol.298 , pp. 799-804
    • Lee, T.I.1
  • 13
    • 33749061959 scopus 로고    scopus 로고
    • Protein binding microarrays (PBMs) for rapid, high-throughput characterization of the sequence specificities of DNA binding proteins
    • Berger M.F., and Bulyk M.L. Protein binding microarrays (PBMs) for rapid, high-throughput characterization of the sequence specificities of DNA binding proteins. Methods Mol. Biol. 338 (2006) 245-260
    • (2006) Methods Mol. Biol. , vol.338 , pp. 245-260
    • Berger, M.F.1    Bulyk, M.L.2
  • 14
    • 1642515774 scopus 로고    scopus 로고
    • Activator protein 2alpha inhibits tumorigenicity and represses vascular endothelial growth factor transcription in prostate cancer cells
    • Ruiz M., et al. Activator protein 2alpha inhibits tumorigenicity and represses vascular endothelial growth factor transcription in prostate cancer cells. Cancer Res. 64 (2004) 631-638
    • (2004) Cancer Res. , vol.64 , pp. 631-638
    • Ruiz, M.1
  • 15
    • 34250159524 scopus 로고    scopus 로고
    • Genome-wide mapping of in vivo protein-DNA interactions
    • Johnson D.S., et al. Genome-wide mapping of in vivo protein-DNA interactions. Science 316 (2007) 1497-1502
    • (2007) Science , vol.316 , pp. 1497-1502
    • Johnson, D.S.1
  • 16
    • 52649132425 scopus 로고    scopus 로고
    • Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data
    • Jothi R., et al. Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res. 36 (2008) 5221-5231
    • (2008) Nucleic Acids Res. , vol.36 , pp. 5221-5231
    • Jothi, R.1
  • 17
    • 19944430797 scopus 로고    scopus 로고
    • Genomic maps and comparative analysis of histone modifications in human and mouse
    • Bernstein B.E., et al. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120 (2005) 169-181
    • (2005) Cell , vol.120 , pp. 169-181
    • Bernstein, B.E.1
  • 18
    • 34547633677 scopus 로고    scopus 로고
    • Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
    • Robertson G., et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods 4 (2007) 651-657
    • (2007) Nat. Methods , vol.4 , pp. 651-657
    • Robertson, G.1
  • 19
    • 36248989105 scopus 로고    scopus 로고
    • ChIP-Seq data reveal nucleosome architecture of human promoters
    • Schmid C.D., and Bucher P. ChIP-Seq data reveal nucleosome architecture of human promoters. Cell 131 (2007) 831-832
    • (2007) Cell , vol.131 , pp. 831-832
    • Schmid, C.D.1    Bucher, P.2
  • 20
    • 0037033984 scopus 로고    scopus 로고
    • The economic and social burden of malaria
    • Sachs J., and Malaney P. The economic and social burden of malaria. Nature 415 (2002) 680-685
    • (2002) Nature , vol.415 , pp. 680-685
    • Sachs, J.1    Malaney, P.2
  • 21
    • 4243071596 scopus 로고    scopus 로고
    • The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum
    • Bozdech Z., et al. The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol. 1 (2003) E5
    • (2003) PLoS Biol. , vol.1
    • Bozdech, Z.1
  • 22
    • 19944429644 scopus 로고    scopus 로고
    • A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses
    • Hall N., et al. A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses. Science 307 (2005) 82-86
    • (2005) Science , vol.307 , pp. 82-86
    • Hall, N.1
  • 23
    • 0141633042 scopus 로고    scopus 로고
    • Discovery of gene function by expression profiling of the malaria parasite life cycle
    • Le Roch K.G., et al. Discovery of gene function by expression profiling of the malaria parasite life cycle. Science 301 (2003) 1503-1508
    • (2003) Science , vol.301 , pp. 1503-1508
    • Le Roch, K.G.1
  • 24
    • 38349159563 scopus 로고    scopus 로고
    • A combined transcriptome and proteome survey of malaria parasite liver stages
    • Tarun A.S., et al. A combined transcriptome and proteome survey of malaria parasite liver stages. Proc. Natl. Acad. Sci. U. S. A. 105 (2008) 305-310
    • (2008) Proc. Natl. Acad. Sci. U. S. A. , vol.105 , pp. 305-310
    • Tarun, A.S.1
  • 25
    • 25444456367 scopus 로고    scopus 로고
    • Prediction of the general transcription factors associated with RNA polymerase II in Plasmodium falciparum: conserved features and differences relative to other eukaryotes
    • Callebaut I., et al. Prediction of the general transcription factors associated with RNA polymerase II in Plasmodium falciparum: conserved features and differences relative to other eukaryotes. BMC Genomics 6 (2005) 100
    • (2005) BMC Genomics , vol.6 , pp. 100
    • Callebaut, I.1
  • 26
    • 4444339460 scopus 로고    scopus 로고
    • Comparative genomics of transcriptional control in the human malaria parasite Plasmodium falciparum
    • Coulson R.M., et al. Comparative genomics of transcriptional control in the human malaria parasite Plasmodium falciparum. Genome Res. 14 (2004) 1548-1554
    • (2004) Genome Res. , vol.14 , pp. 1548-1554
    • Coulson, R.M.1
  • 27
    • 23144448511 scopus 로고    scopus 로고
    • Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains
    • Balaji S., et al. Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains. Nucleic Acids Res. 33 (2005) 3994-4006
    • (2005) Nucleic Acids Res. , vol.33 , pp. 3994-4006
    • Balaji, S.1
  • 28
    • 46149107652 scopus 로고    scopus 로고
    • Specific DNA-binding by apicomplexan AP2 transcription factors
    • De Silva E.K., et al. Specific DNA-binding by apicomplexan AP2 transcription factors. Proc. Natl. Acad. Sci. U. S. A. 105 (2008) 8393-8398
    • (2008) Proc. Natl. Acad. Sci. U. S. A. , vol.105 , pp. 8393-8398
    • De Silva, E.K.1
  • 29
    • 0034651580 scopus 로고    scopus 로고
    • Pathogenesis, natural history, treatment, and prevention of hepatitis C
    • Liang T.J., et al. Pathogenesis, natural history, treatment, and prevention of hepatitis C. Ann. Intern. Med. 132 (2000) 296-305
    • (2000) Ann. Intern. Med. , vol.132 , pp. 296-305
    • Liang, T.J.1
  • 30
    • 33846467150 scopus 로고    scopus 로고
    • A systems approach to measuring the binding energy landscapes of transcription factors
    • Maerkl S.J., and Quake S.R. A systems approach to measuring the binding energy landscapes of transcription factors. Science 315 (2007) 233-237
    • (2007) Science , vol.315 , pp. 233-237
    • Maerkl, S.J.1    Quake, S.R.2
  • 31
    • 0036898579 scopus 로고    scopus 로고
    • Protein microarrays and proteomics
    • MacBeath G. Protein microarrays and proteomics. Nat. Genet. 32 Suppl (2002) 526-532
    • (2002) Nat. Genet. , vol.32 , Issue.SUPPL , pp. 526-532
    • MacBeath, G.1
  • 33
    • 0005620475 scopus 로고    scopus 로고
    • Aptamers as therapeutic and diagnostic agents
    • Brody E.N., and Gold L. Aptamers as therapeutic and diagnostic agents. J. Biotechnol. 74 (2000) 5-13
    • (2000) J. Biotechnol. , vol.74 , pp. 5-13
    • Brody, E.N.1    Gold, L.2
  • 34
    • 0002414180 scopus 로고    scopus 로고
    • In vitro selection of nucleic acids for diagnostic applications
    • Hesselberth J., et al. In vitro selection of nucleic acids for diagnostic applications. J. Biotechnol. 74 (2000) 15-25
    • (2000) J. Biotechnol. , vol.74 , pp. 15-25
    • Hesselberth, J.1
  • 35
    • 0032860385 scopus 로고    scopus 로고
    • Aptamers: an emerging class of molecules that rival antibodies in diagnostics
    • Jayasena S.D. Aptamers: an emerging class of molecules that rival antibodies in diagnostics. Clin. Chem. 45 (1999) 1628-1650
    • (1999) Clin. Chem. , vol.45 , pp. 1628-1650
    • Jayasena, S.D.1
  • 36
    • 34548551398 scopus 로고    scopus 로고
    • SELEX-a (r)evolutionary method to generate high-affinity nucleic acid ligands
    • Stoltenburg R., et al. SELEX-a (r)evolutionary method to generate high-affinity nucleic acid ligands. Biomol. Eng. 24 (2007) 381-403
    • (2007) Biomol. Eng. , vol.24 , pp. 381-403
    • Stoltenburg, R.1
  • 37
    • 0036022523 scopus 로고    scopus 로고
    • High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites
    • Roulet E., et al. High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites. Nat. Biotechnol. 20 (2002) 831-835
    • (2002) Nat. Biotechnol. , vol.20 , pp. 831-835
    • Roulet, E.1
  • 38
    • 0034852021 scopus 로고    scopus 로고
    • Automated selection of anti-protein aptamers
    • Cox J.C., and Ellington A.D. Automated selection of anti-protein aptamers. Bioorg. Med. Chem. 9 (2001) 2525-2531
    • (2001) Bioorg. Med. Chem. , vol.9 , pp. 2525-2531
    • Cox, J.C.1    Ellington, A.D.2
  • 39
    • 0032210799 scopus 로고    scopus 로고
    • Automated RNA selection
    • Cox J.C., et al. Automated RNA selection. Biotechnol. Prog. 14 (1998) 845-850
    • (1998) Biotechnol. Prog. , vol.14 , pp. 845-850
    • Cox, J.C.1
  • 40
    • 33646352484 scopus 로고    scopus 로고
    • Characterization and application of a novel RNA aptamer against the mouse prion protein
    • Sekiya S., et al. Characterization and application of a novel RNA aptamer against the mouse prion protein. J. Biochem. 139 (2006) 383-390
    • (2006) J. Biochem. , vol.139 , pp. 383-390
    • Sekiya, S.1
  • 41
    • 33644597254 scopus 로고    scopus 로고
    • An RNA aptamer that distinguishes between closely related human influenza viruses and inhibits haemagglutinin-mediated membrane fusion
    • Gopinath S.C., et al. An RNA aptamer that distinguishes between closely related human influenza viruses and inhibits haemagglutinin-mediated membrane fusion. J. Gen. Virol. 87 (2006) 479-487
    • (2006) J. Gen. Virol. , vol.87 , pp. 479-487
    • Gopinath, S.C.1
  • 42
    • 33745746584 scopus 로고    scopus 로고
    • An efficient RNA aptamer against human influenza B virus hemagglutinin
    • Gopinath S.C., et al. An efficient RNA aptamer against human influenza B virus hemagglutinin. J. Biochem. 139 (2006) 837-846
    • (2006) J. Biochem. , vol.139 , pp. 837-846
    • Gopinath, S.C.1
  • 43
    • 38849205404 scopus 로고    scopus 로고
    • DNA aptamers against the MUC1 tumour marker: design of aptamer-antibody sandwich ELISA for the early diagnosis of epithelial tumours
    • Ferreira C.S., et al. DNA aptamers against the MUC1 tumour marker: design of aptamer-antibody sandwich ELISA for the early diagnosis of epithelial tumours. Anal. Bioanal. Chem. 390 (2008) 1039-1050
    • (2008) Anal. Bioanal. Chem. , vol.390 , pp. 1039-1050
    • Ferreira, C.S.1
  • 44
    • 13644266857 scopus 로고    scopus 로고
    • Functional RNA microarrays for high-throughput screening of antiprotein aptamers
    • Collett J.R., et al. Functional RNA microarrays for high-throughput screening of antiprotein aptamers. Anal. Biochem. 338 (2005) 113-123
    • (2005) Anal. Biochem. , vol.338 , pp. 113-123
    • Collett, J.R.1
  • 45
    • 24644458830 scopus 로고    scopus 로고
    • Aptamer-derived nucleic acid oligos: applications to develop nucleic acid chips to analyze proteins and small ligands
    • Yamamoto-Fujita R., and Kumar P.K. Aptamer-derived nucleic acid oligos: applications to develop nucleic acid chips to analyze proteins and small ligands. Anal. Chem. 77 (2005) 5460-5466
    • (2005) Anal. Chem. , vol.77 , pp. 5460-5466
    • Yamamoto-Fujita, R.1    Kumar, P.K.2
  • 46
    • 0346495950 scopus 로고    scopus 로고
    • Aptamer database
    • Lee J.F., et al. Aptamer database. Nucleic Acids Res. 32 Database issue (2004) D95-D100
    • (2004) Nucleic Acids Res. , vol.32 , Issue.Database issue
    • Lee, J.F.1
  • 48
    • 53049087109 scopus 로고    scopus 로고
    • Genomic and epigenetic instability in colorectal cancer pathogenesis
    • Grady W.M., and Carethers J.M. Genomic and epigenetic instability in colorectal cancer pathogenesis. Gastroenterology. 135 (2008) 1079-1099
    • (2008) Gastroenterology. , vol.135 , pp. 1079-1099
    • Grady, W.M.1    Carethers, J.M.2
  • 49
    • 24144491073 scopus 로고    scopus 로고
    • Optimization of reporter cells for expression profiling in a microfluidic device
    • Wieder K.J., et al. Optimization of reporter cells for expression profiling in a microfluidic device. Biomed. Microdevices 7 (2005) 213-222
    • (2005) Biomed. Microdevices , vol.7 , pp. 213-222
    • Wieder, K.J.1
  • 50
    • 36448935709 scopus 로고    scopus 로고
    • Versatile, fully automated, microfluidic cell culture system
    • Gomez-Sjoberg R., et al. Versatile, fully automated, microfluidic cell culture system. Anal. Chem. 79 (2007) 8557-8563
    • (2007) Anal. Chem. , vol.79 , pp. 8557-8563
    • Gomez-Sjoberg, R.1
  • 51
    • 0034934774 scopus 로고    scopus 로고
    • Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association
    • Lieb J.D., et al. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat. Genet. 28 (2001) 327-334
    • (2001) Nat. Genet. , vol.28 , pp. 327-334
    • Lieb, J.D.1
  • 52
    • 0035945567 scopus 로고    scopus 로고
    • Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF
    • Iyer V.R., et al. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409 (2001) 533-538
    • (2001) Nature , vol.409 , pp. 533-538
    • Iyer, V.R.1
  • 53
    • 0034515772 scopus 로고    scopus 로고
    • Coordinate regulation of yeast ribosomal protein genes is associated with targeted recruitment of Esa1 histone acetylase
    • Reid J.L., et al. Coordinate regulation of yeast ribosomal protein genes is associated with targeted recruitment of Esa1 histone acetylase. Mol. Cell 6 (2000) 1297-1307
    • (2000) Mol. Cell , vol.6 , pp. 1297-1307
    • Reid, J.L.1
  • 54
    • 0034704248 scopus 로고    scopus 로고
    • Genome-wide location and function of DNA binding proteins
    • Ren B., et al. Genome-wide location and function of DNA binding proteins. Science 290 (2000) 2306-2309
    • (2000) Science , vol.290 , pp. 2306-2309
    • Ren, B.1
  • 55
    • 0034007256 scopus 로고    scopus 로고
    • Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase
    • van Steensel B., and Henikoff S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat. Biotechnol. 18 (2000) 424-428
    • (2000) Nat. Biotechnol. , vol.18 , pp. 424-428
    • van Steensel, B.1    Henikoff, S.2
  • 56
    • 0035093828 scopus 로고    scopus 로고
    • Chromatin profiling using targeted DNA adenine methyltransferase
    • van Steensel B., et al. Chromatin profiling using targeted DNA adenine methyltransferase. Nat. Genet. 27 (2001) 304-308
    • (2001) Nat. Genet. , vol.27 , pp. 304-308
    • van Steensel, B.1
  • 57
    • 46949098742 scopus 로고    scopus 로고
    • A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
    • Down T.A., et al. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat. Biotechnol. 26 (2008) 779-785
    • (2008) Nat. Biotechnol. , vol.26 , pp. 779-785
    • Down, T.A.1
  • 58
    • 56549101959 scopus 로고    scopus 로고
    • Alternative isoform regulation in human tissue transcriptomes
    • Wang E.T., et al. Alternative isoform regulation in human tissue transcriptomes. Nature 456 (2008) 470-476
    • (2008) Nature , vol.456 , pp. 470-476
    • Wang, E.T.1
  • 59
    • 47649124124 scopus 로고    scopus 로고
    • A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome
    • Sultan M., et al. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 321 (2008) 956-960
    • (2008) Science , vol.321 , pp. 956-960
    • Sultan, M.1
  • 60
    • 50649089207 scopus 로고    scopus 로고
    • RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays
    • Marioni J.C., et al. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res. 18 (2008) 1509-1517
    • (2008) Genome Res. , vol.18 , pp. 1509-1517
    • Marioni, J.C.1


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