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Volumn 5, Issue , 2015, Pages

Correcting positional correlations in Affymetrix® Genome Chips

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[No Author keywords available]

Indexed keywords

DNA PROBE;

EID: 84924873520     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep09078     Document Type: Article
Times cited : (3)

References (33)
  • 1
    • 84984932472 scopus 로고    scopus 로고
    • Exploring the new world of the genome with DNA microarrays
    • Brown, P. O. & Botstein, D. Exploring the new world of the genome with DNA microarrays. Nature Genet. 21, 33-37 (1999).
    • (1999) Nature Genet. , vol.21 , pp. 33-37
    • Brown, P.O.1    Botstein, D.2
  • 2
    • 0031963203 scopus 로고    scopus 로고
    • DNA chips: State-of-the-art
    • Ramsay, G. DNA chips: State-of-the-art. Nature Biotechnology 16, 40-44 (1998).
    • (1998) Nature Biotechnology , vol.16 , pp. 40-44
    • Ramsay, G.1
  • 3
    • 84984934048 scopus 로고    scopus 로고
    • DNA microarrays in drug discovery and development
    • Debouck, C. & Goodfellow, P. N. DNA microarrays in drug discovery and development. Nature Genet. 21, 48-50 (1999).
    • (1999) Nature Genet. , vol.21 , pp. 48-50
    • Debouck, C.1    Goodfellow, P.N.2
  • 4
    • 0036405278 scopus 로고    scopus 로고
    • DNA microarray technology: Devices, systems, and applications
    • Heller, M. J. DNA microarray technology: Devices, systems, and applications. Annual Review of Biomedical Engineering 4, 129-153, doi:10.1146/ annurev.bioeng.4.020702.153438 (2002).
    • (2002) Annual Review of Biomedical Engineering , vol.4 , pp. 129-153
    • Heller, M.J.1
  • 5
    • 0029852580 scopus 로고    scopus 로고
    • Use of a cDNA microarray to analyse gene expression patterns in human cancer
    • DeRisi, J. et al. Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nature Genet. 14, 457-460 (1996).
    • (1996) Nature Genet. , vol.14 , pp. 457-460
    • DeRisi, J.1
  • 6
    • 0036884167 scopus 로고    scopus 로고
    • The use and analysis of microarray data
    • Butte, A. The use and analysis of microarray data. Nature Reviews Drug Discovery 1, 951-960, doi:10.1038/nrd.961 (2002).
    • (2002) Nature Reviews Drug Discovery , vol.1 , pp. 951-960
    • Butte, A.1
  • 7
    • 33644844520 scopus 로고    scopus 로고
    • Microarray technology: Beyond transcript profiling and genotype analysis
    • Hoheisel, J. D. Microarray technology: beyond transcript profiling and genotype analysis. Nature Reviews Genetics 7, 200-210, doi:10.1038/nrg1809 (2006).
    • (2006) Nature Reviews Genetics , vol.7 , pp. 200-210
    • Hoheisel, J.D.1
  • 9
    • 0033031437 scopus 로고    scopus 로고
    • Cdna Preparation and Characterization
    • Academic Press Inc
    • Eisen, M. B. & Brown, P. O. in Cdna Preparation and Characterization Vol. 303 Methods in Enzymology 179-205 (Academic Press Inc, 1999).
    • (1999) Methods in Enzymology , vol.303 , pp. 179-205
    • Eisen, M.B.1    Brown, P.O.2
  • 10
    • 0037323796 scopus 로고    scopus 로고
    • Microarray expression profiling: Capturing a genome-wide portrait of the transcriptome
    • Conway, T. & Schoolnik, G. K. Microarray expression profiling: capturing a genome-wide portrait of the transcriptome. Molecular Microbiology 47, 879-889 (2003).
    • (2003) Molecular Microbiology , vol.47 , pp. 879-889
    • Conway, T.1    Schoolnik, G.K.2
  • 12
    • 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 270, 467-470 (1995).
    • (1995) Science , vol.270 , pp. 467-470
    • Schena, M.1    Shalon, D.2    Davis, R.W.3    Brown, P.O.4
  • 13
    • 13444304325 scopus 로고    scopus 로고
    • NCBI GEO: Miningmillions of expression profiles - Database and tools
    • Barrett, T. et al. NCBI GEO: miningmillions of expression profiles - database and tools. Nucleic Acids Res. 33, D562-D566 (2005).
    • (2005) Nucleic Acids Res. , vol.33 , pp. D562-D566
    • Barrett, T.1
  • 14
    • 0038492417 scopus 로고    scopus 로고
    • Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae)
    • Troyanskaya, O. G., Dolinski, K., Owen, A. B., Altman, R. B. & Botstein, D. A. Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae). Proc. Natl. Acad. Sci. U. S. A. 100, 8348-8353, doi:10.1073/pnas.0832373100 (2003).
    • (2003) Proc. Natl. Acad. Sci. U. S. A. , vol.100 , pp. 8348-8353
    • Troyanskaya, O.G.1    Dolinski, K.2    Owen, A.B.3    Altman, R.B.4    Botstein, D.A.5
  • 15
    • 33745113181 scopus 로고    scopus 로고
    • Discovery of biological networks from diverse functional genomic data
    • Myers, C. L. et al. Discovery of biological networks from diverse functional genomic data. Genome Biology 6, 16, doi:R114.10.1186/gb-2005-6-13-r114 (2005).
    • (2005) Genome Biology , vol.6 , pp. 16
    • Myers, C.L.1
  • 16
    • 84899464281 scopus 로고    scopus 로고
    • Modulation of Gene Expression Regulated by the Transcription Factor NF-kB/RelA
    • Li, X. et al.Modulation of Gene Expression Regulated by the Transcription Factor NF-kB/RelA. Journal of Biological Chemistry 289, 11927-11944 (2014).
    • (2014) Journal of Biological Chemistry , vol.289 , pp. 11927-11944
    • Li, X.1
  • 17
    • 33750353888 scopus 로고    scopus 로고
    • Reverse engineering cellular networks
    • Margolin, A. A. et al. Reverse engineering cellular networks. Nature protocols 1, 662-671 (2006).
    • (2006) Nature protocols , vol.1 , pp. 662-671
    • Margolin, A.A.1
  • 18
    • 84855160951 scopus 로고    scopus 로고
    • Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information
    • Zhang, X. et al. Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information. Bioinformatics 28, 98-104 (2012).
    • (2012) Bioinformatics , vol.28 , pp. 98-104
    • Zhang, X.1
  • 21
    • 36448948634 scopus 로고    scopus 로고
    • Systematic order-dependent effect in expression values, variance, detection calls and differential expression in Affymetrix GeneChips (R)
    • Bjork, K. E. & Kafadar, K. Systematic order-dependent effect in expression values, variance, detection calls and differential expression in Affymetrix GeneChips (R). Bioinformatics 23, 2873-2880, doi:10.1093/bioinformatics/btm450 (2007).
    • (2007) Bioinformatics , vol.23 , pp. 2873-2880
    • Bjork, K.E.1    Kafadar, K.2
  • 22
    • 65549170677 scopus 로고    scopus 로고
    • Probes containing runs of guanines provide insights into the biophysics and bioinformatics of Affymetrix GeneChips
    • Langdon, W. B., Upton, G. J. G. & Harrison, A. P. Probes containing runs of guanines provide insights into the biophysics and bioinformatics of Affymetrix GeneChips. Briefings in Bioinformatics 10, 259-277, doi:10.1093/bib/bbp018 (2009).
    • (2009) Briefings in Bioinformatics , vol.10 , pp. 259-277
    • Langdon, W.B.1    Upton, G.J.G.2    Harrison, A.P.3
  • 24
    • 33846938060 scopus 로고    scopus 로고
    • Positional artifacts in microarrays: Experimental verification and construction of COP, an automated detection tool
    • Yu, H. et al. Positional artifacts in microarrays: experimental verification and construction of COP, an automated detection tool. Nucleic Acids Res. 35, E8 (2007).
    • (2007) Nucleic Acids Res. , vol.35 , pp. E8
    • Yu, H.1
  • 25
    • 0038002409 scopus 로고    scopus 로고
    • Identification and correction of spurious spatial correlations in microarray data
    • Qian, J., Kluger, Y., Yu, H.&Gerstein, M. Identification and correction of spurious spatial correlations in microarray data. Biotechniques 35, 42-48 (2003).
    • (2003) Biotechniques , vol.35 , pp. 42-48
    • Qian, J.1    Kluger, Y.2    Yu, H.3    Gerstein, M.4
  • 26
    • 9444236735 scopus 로고    scopus 로고
    • Relationship between gene coexpression and probe localization on microarray slides
    • Kluger, Y., Yu, H., Qian, J. & Gerstein, M. Relationship between gene coexpression and probe localization on microarray slides. Bmc Genomics 4, 49, doi:10.1186/1471-2164-4-49 (2003).
    • (2003) Bmc Genomics , vol.4 , pp. 49
    • Kluger, Y.1    Yu, H.2    Qian, J.3    Gerstein, M.4
  • 27
    • 0034161444 scopus 로고    scopus 로고
    • Regulation of adjacent yeast genes
    • Kruglyak, S. & Tang, H. X. Regulation of adjacent yeast genes. Trends in Genetics 16, 109-111 (2000).
    • (2000) Trends in Genetics , vol.16 , pp. 109-111
    • Kruglyak, S.1    Tang, H.X.2
  • 28
    • 57349140010 scopus 로고    scopus 로고
    • Transcriptional regulation constrains the organization of genes on eukaryotic chromosomes
    • Janga, S. C., Collado-Vides, J.&Babu, M. M. Transcriptional regulation constrains the organization of genes on eukaryotic chromosomes. Proc. Natl. Acad. Sci. U. S. A. 105, 15761-15766, doi:10.1073/pnas.0806317105 (2008).
    • (2008) Proc. Natl. Acad. Sci. U. S. A. , vol.105 , pp. 15761-15766
    • Janga, S.C.1    Collado-Vides, J.2    Babu, M.M.3
  • 29
    • 0036855423 scopus 로고    scopus 로고
    • SNOMAD (Standardization and NOrmalization of MicroArray Data): Web-accessible gene expression data analysis
    • Colantuoni, C., Henry, G., Zeger, S. & Pevsner, J. SNOMAD (Standardization and NOrmalization of MicroArray Data): web-accessible gene expression data analysis. Bioinformatics 18, 1540-1541 (2002).
    • (2002) Bioinformatics , vol.18 , pp. 1540-1541
    • Colantuoni, C.1    Henry, G.2    Zeger, S.3    Pevsner, J.4
  • 30
    • 28744458859 scopus 로고    scopus 로고
    • Bioconductor: Open software development for computational biology and bioinformatics
    • Gentleman, R. C. et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biology 5, -, doi:Artn R80 (2004).
    • (2004) Genome Biology , vol.5
    • Gentleman, R.C.1
  • 31
    • 27944487902 scopus 로고    scopus 로고
    • Logic of the yeast metabolic cycle: Temporal compartmentalization of cellular processes
    • Tu, B. P., Kudlicki, A., Rowicka, M. & McKnight, S. L. Logic of the yeast metabolic cycle: Temporal compartmentalization of cellular processes. Science 310, 1152-1158, doi:10.1126/science.1120499 (2005).
    • (2005) Science , vol.310 , pp. 1152-1158
    • Tu, B.P.1    Kudlicki, A.2    Rowicka, M.3    McKnight, S.L.4
  • 32
    • 33644873683 scopus 로고    scopus 로고
    • The YEASTRACT database: A tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae
    • Teixeira, M. C. et al. The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Res. 34, D446-D451, doi:10.1093/nar/gkj013 (2006).
    • (2006) Nucleic Acids Res. , vol.34 , pp. D446-D451
    • Teixeira, M.C.1
  • 33
    • 4544352942 scopus 로고    scopus 로고
    • Transcriptional regulatory code of a eukaryotic genome
    • Harbison, C. T. et al. Transcriptional regulatory code of a eukaryotic genome. Nature 431, 99-104, doi:10.1038/nature02800 (2004).
    • (2004) Nature , vol.431 , pp. 99-104
    • Harbison, C.T.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.