메뉴 건너뛰기




Volumn 23, Issue 8, 2007, Pages 988-997

Assessing the need for sequence-based normalization in tiling microarray experiments

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

EID: 34249730556     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btm052     Document Type: Article
Times cited : (35)

References (32)
  • 1
    • 0016061478 scopus 로고
    • The fitting of power series, meaning polynomials, illustrated on band-spectroscopic data
    • Beaton,A.E. and Tukey,J.W. (1974) The fitting of power series, meaning polynomials, illustrated on band-spectroscopic data. Technometrics 16, 147-185.
    • (1974) Technometrics , vol.16 , pp. 147-185
    • Beaton, A.E.1    Tukey, J.W.2
  • 2
    • 19944376457 scopus 로고    scopus 로고
    • Global identification of human transcribed sequences with genome tiling arrays
    • Bertone,P. et al. (2004) Global identification of human transcribed sequences with genome tiling arrays. Science, 306 2242-2246.
    • (2004) Science , vol.306 , pp. 2242-2246
    • Bertone, P.1
  • 3
    • 0037316303 scopus 로고    scopus 로고
    • A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    • Bolstad,B.M. et al. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics, 19, 185-193.
    • (2003) Bioinformatics , vol.19 , pp. 185-193
    • Bolstad, B.M.1
  • 4
    • 10744226888 scopus 로고    scopus 로고
    • Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs
    • Cawley,S. et al. (2004) Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell, 116, 499-509.
    • (2004) Cell , vol.116 , pp. 499-509
    • Cawley, S.1
  • 5
    • 10244219858 scopus 로고    scopus 로고
    • Accessing genetic information with high-density DNA arrays
    • Chee,M. et al. (1996) Accessing genetic information with high-density DNA arrays. Science, 274, 610-614.
    • (1996) Science , vol.274 , pp. 610-614
    • Chee, M.1
  • 6
    • 84936916896 scopus 로고
    • Robust locally weighted regression and smoothing scatterplots
    • Cleveland,W.S. (1979) Robust locally weighted regression and smoothing scatterplots. J. Am. Stat. Assoc., 74, 829-836.
    • (1979) J. Am. Stat. Assoc , vol.74 , pp. 829-836
    • Cleveland, W.S.1
  • 7
    • 33645785104 scopus 로고    scopus 로고
    • A high-resolution map of transcription in the yeast genome
    • David,L. et al. (2006) A high-resolution map of transcription in the yeast genome. Proc. Natl Acad. Sci. USA, 103, 5320-5325.
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 5320-5325
    • David, L.1
  • 8
    • 33748493610 scopus 로고    scopus 로고
    • Replacing cRNA targets with cDNA reduces microarry cross-hybridization
    • Eklund,A.C. et al. (2006) Replacing cRNA targets with cDNA reduces microarry cross-hybridization. Nat. Biotechnol., 24, 1071-1073.
    • (2006) Nat. Biotechnol , vol.24 , pp. 1071-1073
    • Eklund, A.C.1
  • 9
    • 34447313213 scopus 로고    scopus 로고
    • Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome
    • November 21 Epub ahead of print
    • Emanuelsson,O. et al. (2006) Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome. Genome. Res., November 21 (Epub ahead of print).
    • (2006) Genome. Res
    • Emanuelsson, O.1
  • 10
    • 7444260846 scopus 로고    scopus 로고
    • The ENCODE (ENCyclopedia Of DNA Elements) Project
    • ENCODE Consortium
    • ENCODE Consortium (2004) The ENCODE (ENCyclopedia Of DNA Elements) Project. Science, 306, 636-640.
    • (2004) Science , vol.306 , pp. 636-640
  • 11
    • 33748645500 scopus 로고    scopus 로고
    • GENCODE: Producing a reference annotation for ENCODE
    • Harrow,J. et al. (2006) GENCODE: Producing a reference annotation for ENCODE. Genome. Biol., 7 (Suppl. 1), S4.1-S4.9.
    • (2006) Genome. Biol , vol.7 , Issue.SUPPL. 1
    • Harrow, J.1
  • 12
    • 0037388263 scopus 로고    scopus 로고
    • Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide arrays
    • Hekstra,D. et al. (2003) Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide arrays. Nucleic Acids Res., 31, 1962-1968.
    • (2003) Nucleic Acids Res , vol.31 , pp. 1962-1968
    • Hekstra, D.1
  • 13
    • 0036894656 scopus 로고    scopus 로고
    • Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae
    • Horak,C.E. et al. (2002) Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes. Dev., 16 3017-3033.
    • (2002) Genes. Dev , vol.16 , pp. 3017-3033
    • Horak, C.E.1
  • 14
    • 33747856481 scopus 로고    scopus 로고
    • Transcript mapping with high-density oligonucleotide tiling arrays
    • Huber,W. et al. (2006) Transcript mapping with high-density oligonucleotide tiling arrays. Bioinformatics, 22, 1963-1970.
    • (2006) Bioinformatics , vol.22 , pp. 1963-1970
    • Huber, W.1
  • 15
    • 12344280017 scopus 로고    scopus 로고
    • Summaries of affymetrix GeneChip probe level data
    • Irizarry,R.A. et al. (2003) Summaries of affymetrix GeneChip probe level data. Nucleic Acids Res., 31, e15.
    • (2003) Nucleic Acids Res , vol.31
    • Irizarry, R.A.1
  • 16
    • 12344291073 scopus 로고    scopus 로고
    • Dark matter in the genome: Evidence of widespread transcription detected by microarray tiling experiments
    • Johnson,J.M. et al. (2005) Dark matter in the genome: Evidence of widespread transcription detected by microarray tiling experiments. Trends Genet., 21, 93-102.
    • (2005) Trends Genet , vol.21 , pp. 93-102
    • Johnson, J.M.1
  • 17
    • 12144287461 scopus 로고    scopus 로고
    • Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22
    • Kampa,D. et al. (2004) Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res., 14, 331-342.
    • (2004) Genome Res , vol.14 , pp. 331-342
    • Kampa, D.1
  • 18
    • 0037012881 scopus 로고    scopus 로고
    • Large-scale transcriptional activity in chromosomes 21 and 22
    • Kapranov,P. et al. (2002) Large-scale transcriptional activity in chromosomes 21 and 22. Science, 296, 916-919.
    • (2002) Science , vol.296 , pp. 916-919
    • Kapranov, P.1
  • 19
    • 0036226603 scopus 로고    scopus 로고
    • BLAT - the BLAST-like alignment tool
    • Kent,W.J. (2002) BLAT - the BLAST-like alignment tool. Genome Res. 12, 656-664.
    • (2002) Genome Res , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 20
    • 0035793042 scopus 로고    scopus 로고
    • Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection
    • Li,C. and Wong,W.H. (2001) Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection. Proc. Natl Acad. Sci. USA, 98, 31-36.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 31-36
    • Li, C.1    Wong, W.H.2
  • 21
    • 84984933234 scopus 로고    scopus 로고
    • High density synthetic oligonucleotide arrays
    • Lipshutz,R.J. et al. (1999) High density synthetic oligonucleotide arrays: Nat. Genet, 21 (Suppl. 1), 20-24.
    • (1999) Nat. Genet , vol.21 , Issue.SUPPL. 1 , pp. 20-24
    • Lipshutz, R.J.1
  • 22
    • 10644247621 scopus 로고    scopus 로고
    • Applications of DNA tiling arrays for whole-genome analysis
    • Mockler,T.C. et al. (2005) Applications of DNA tiling arrays for whole-genome analysis. Genomics, 85, 1-15.
    • (2005) Genomics , vol.85 , pp. 1-15
    • Mockler, T.C.1
  • 23
    • 33745295639 scopus 로고    scopus 로고
    • A hidden Markov model approach for determining expression from genomic tiling micro arrays
    • Munch,K. et al. (2006) A hidden Markov model approach for determining expression from genomic tiling micro arrays. BMC Bioinformatics, 7, 239.
    • (2006) BMC Bioinformatics , vol.7 , pp. 239
    • Munch, K.1
  • 24
    • 85035214096 scopus 로고    scopus 로고
    • Solving the riddle of the bright mismatches: Labeling and effective binding in oligonucleotide arrays
    • Naef,F. and Magnasco,M.O. (2003) Solving the riddle of the bright mismatches: Labeling and effective binding in oligonucleotide arrays. Phys. Rev. E. Stat. Nonlin. Soft Matter Phys., 68, 011906.
    • (2003) Phys. Rev. E. Stat. Nonlin. Soft Matter Phys , vol.68 , pp. 011906
    • Naef, F.1    Magnasco, M.O.2
  • 25
    • 0037442493 scopus 로고    scopus 로고
    • The transcriptional activity of human chromosome 22
    • Rinn,J.L. et al. (2003) The transcriptional activity of human chromosome 22. Genes Dev., 17, 529-540.
    • (2003) Genes Dev , vol.17 , pp. 529-540
    • Rinn, J.L.1
  • 26
    • 22144467302 scopus 로고    scopus 로고
    • Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping
    • Royce,T.E. et al. (2005) Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. Trends Genet., 21 466-475.
    • (2005) Trends Genet , vol.21 , pp. 466-475
    • Royce, T.E.1
  • 27
    • 33645229776 scopus 로고    scopus 로고
    • Global identification of noncoding RNAs in Saccharomyces cerevisiae by modulating an essential RNA processing pathway
    • Samanta,M.P. et al. (2006) Global identification of noncoding RNAs in Saccharomyces cerevisiae by modulating an essential RNA processing pathway. Proc. Natl. Acad. Sci. USA, 103, 4192-4197.
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 4192-4197
    • Samanta, M.P.1
  • 28
    • 0028806048 scopus 로고
    • Quantitative monitoring of gene expression patterns with a complementary DNA microarray
    • Schena,M. et al. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science, 270, 467-470.
    • (1995) Science , vol.270 , pp. 467-470
    • Schena, M.1
  • 29
    • 0033664358 scopus 로고    scopus 로고
    • RNA expression analysis using a 30 base pair resolution Escherichia coli genome array
    • Selinger,D.W. et al. (2000) RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat. Biotechnol. 18, 1262-1268.
    • (2000) Nat. Biotechnol , vol.18 , pp. 1262-1268
    • Selinger, D.W.1
  • 30
    • 0035865260 scopus 로고    scopus 로고
    • Experimental annotation of the human genome using microarray technology
    • Shoemaker,D.D. et al. (2001) Experimental annotation of the human genome using microarray technology. Nature, 409, 922-927.
    • (2001) Nature , vol.409 , pp. 922-927
    • Shoemaker, D.D.1
  • 31
    • 23844551199 scopus 로고    scopus 로고
    • Stochastic models inspired by hybridization theory for short oligonucleotide arrays
    • Wu,Z. and Irizarry,R.A. (2005) Stochastic models inspired by hybridization theory for short oligonucleotide arrays. J. Comput. Biol., 12, 882-893.
    • (2005) J. Comput. Biol , vol.12 , pp. 882-893
    • Wu, Z.1    Irizarry, R.A.2
  • 32
    • 0038729666 scopus 로고    scopus 로고
    • A model of molecular interactions on short oligonucleotide microarrays
    • Zhang,L. et al. (2003) A model of molecular interactions on short oligonucleotide microarrays. Nat. Biotechnol., 21, 818-821.
    • (2003) Nat. Biotechnol , vol.21 , pp. 818-821
    • Zhang, L.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.