메뉴 건너뛰기




Volumn 6, Issue 1, 2011, Pages

Cross-platform comparison of microarray-based multiple-class prediction

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER;

EID: 79251586838     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0016067     Document Type: Article
Times cited : (16)

References (30)
  • 1
    • 74549174585 scopus 로고    scopus 로고
    • DNA microarrays are predictive of cancer prognosis: A reevaluation
    • Fan XH, Shi LM, Fang H, Cheng YY, Perkins RG, et al. (2010) DNA microarrays are predictive of cancer prognosis: A reevaluation. Clin Cancer Res 16: 629-636.
    • (2010) Clin Cancer Res , vol.16 , pp. 629-636
    • Fan, X.H.1    Shi, L.M.2    Fang, H.3    Cheng, Y.Y.4    Perkins, R.G.5
  • 2
    • 62849091464 scopus 로고    scopus 로고
    • Omic profiling for drug safety assessment: Current trends and public-private partnerships
    • Gallagher WM, Tweats D, Koenig J (2009) Omic profiling for drug safety assessment: current trends and public-private partnerships. Drug Discov Today 14: 337-342.
    • (2009) Drug Discov Today , vol.14 , pp. 337-342
    • Gallagher, W.M.1    Tweats, D.2    Koenig, J.3
  • 3
    • 40849097774 scopus 로고    scopus 로고
    • Comparing whole genomes using DNA microarrays
    • Gresham D, Dunham MJ, Botstein D (2008) Comparing whole genomes using DNA microarrays. Nat Rev Genet 9: 291-302.
    • (2008) Nat Rev Genet , vol.9 , pp. 291-302
    • Gresham, D.1    Dunham, M.J.2    Botstein, D.3
  • 4
    • 34548329530 scopus 로고    scopus 로고
    • A perspective on DNA microarrays in pathology research and practice
    • Pollack JR (2007) A perspective on DNA microarrays in pathology research and practice. Am J Pathol 171: 375-385.
    • (2007) Am J Pathol , vol.171 , pp. 375-385
    • Pollack, J.R.1
  • 5
    • 39149111585 scopus 로고    scopus 로고
    • Reproducible and reliable microarray results through quality control: Good laboratory proficiency and appropriate data analysis practices are essential
    • Shi LM, Perkins RG, Fang H, Tong WD (2008) Reproducible and reliable microarray results through quality control: good laboratory proficiency and appropriate data analysis practices are essential. Curr Opin Biotechnol 19: 10-18.
    • (2008) Curr Opin Biotechnol , vol.19 , pp. 10-18
    • Shi, L.M.1    Perkins, R.G.2    Fang, H.3    Tong, W.D.4
  • 6
    • 34347337394 scopus 로고    scopus 로고
    • Review of the literature examining the correlation among DNA microarray technologies
    • Yauk CL, Berndt ML (2007) Review of the literature examining the correlation among DNA microarray technologies. Environ Mol Mutagen 48: 380-394.
    • (2007) Environ Mol Mutagen , vol.48 , pp. 380-394
    • Yauk, C.L.1    Berndt, M.L.2
  • 7
    • 0035072249 scopus 로고    scopus 로고
    • Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer
    • Hughes TR, Mao M, Jones AR, Burchard J, Marton MJ, et al. (2001) Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol 19: 342-347.
    • (2001) Nat Biotechnol , vol.19 , pp. 342-347
    • Hughes, T.R.1    Mao, M.2    Jones, A.R.3    Burchard, J.4    Marton, M.J.5
  • 8
    • 0034669668 scopus 로고    scopus 로고
    • Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays
    • Kane MD, Jatkoe TA, Stumpf CR, Lu J, Thomas JD, et al. (2000) Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucleic Acids Res 28: 4552-4557.
    • (2000) Nucleic Acids Res , vol.28 , pp. 4552-4557
    • Kane, M.D.1    Jatkoe, T.A.2    Stumpf, C.R.3    Lu, J.4    Thomas, J.D.5
  • 11
  • 12
    • 0141905890 scopus 로고    scopus 로고
    • Evaluation of gene expression measurements from commercial microarray platforms
    • Tan PK, Downey TJ, Spitznagel EL, Xu P, Fu D, et al. (2003) Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res 31: 5676-5684.
    • (2003) Nucleic Acids Res , vol.31 , pp. 5676-5684
    • Tan, P.K.1    Downey, T.J.2    Spitznagel, E.L.3    Xu, P.4    Fu, D.5
  • 13
    • 27644528185 scopus 로고    scopus 로고
    • Cross-platform comparability of microarray technology: Intra-platform consistency and appropriate data analysis procedures are essential
    • Shi LM, Tong WD, Fang H, Scherf U, Han J, et al. (2005) Cross-platform comparability of microarray technology: Intra-platform consistency and appropriate data analysis procedures are essential. BMC Bioinformatics 6(Suppl 2): S12.
    • (2005) BMC Bioinformatics , vol.6 , Issue.SUPPL. 2
    • Shi, L.M.1    Tong, W.D.2    Fang, H.3    Scherf, U.4    Han, J.5
  • 14
    • 33748495591 scopus 로고    scopus 로고
    • Rat toxicogenomic study reveals analytical consistency across microarray platforms
    • Guo L, Lobenhofer EK, Wang C, Shippy R, Harris SC, et al. (2006) Rat toxicogenomic study reveals analytical consistency across microarray platforms. Nat Biotechnol 24: 1162-1169.
    • (2006) Nat Biotechnol , vol.24 , pp. 1162-1169
    • Guo, L.1    Lobenhofer, E.K.2    Wang, C.3    Shippy, R.4    Harris, S.C.5
  • 15
    • 65449137889 scopus 로고    scopus 로고
    • Evaluation of inter-laboratory and rossplatform concordance of DNA microarrays through discriminating genes and classifier transferability
    • Mao SH, Wang C, Dong GZ (2009) Evaluation of inter-laboratory and rossplatform concordance of DNA microarrays through discriminating genes and classifier transferability. J Bioinform Comput Biol 7: 157-173.
    • (2009) J Bioinform Comput Biol , vol.7 , pp. 157-173
    • Mao, S.H.1    Wang, C.2    Dong, G.Z.3
  • 16
    • 33748491517 scopus 로고    scopus 로고
    • The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
    • Shi LM, Reid LH, Jones WD, Shippy R, Warrington JA, et al. (2006) The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 24: 1151-1161.
    • (2006) Nat Biotechnol , vol.24 , pp. 1151-1161
    • Shi, L.M.1    Reid, L.H.2    Jones, W.D.3    Shippy, R.4    Warrington, J.A.5
  • 17
    • 0037245343 scopus 로고    scopus 로고
    • Pitfalls in the use of DNA microarray data for diagnostic and prognostic classification
    • Simon R, Radmacher MD, Dobbin K, McShane LM (2003) Pitfalls in the use of DNA microarray data for diagnostic and prognostic classification. J Natl Cancer Inst 95: 14-18.
    • (2003) J Natl Cancer Inst , vol.95 , pp. 14-18
    • Simon, R.1    Radmacher, M.D.2    Dobbin, K.3    McShane, L.M.4
  • 18
    • 33846889777 scopus 로고    scopus 로고
    • Multiple gene expression classifiers from different array platforms predict poor prognosis of colorectal cancer
    • Lin YH, Friederichs J, Black MA, Mages J, Rosenberg R, et al. (2007) Multiple gene expression classifiers from different array platforms predict poor prognosis of colorectal cancer. Clin Cancer Res 13: 498-507.
    • (2007) Clin Cancer Res , vol.13 , pp. 498-507
    • Lin, Y.H.1    Friederichs, J.2    Black, M.A.3    Mages, J.4    Rosenberg, R.5
  • 19
    • 77955127780 scopus 로고    scopus 로고
    • Consistency of Predictive Signature Genes and Classifiers Generated Using Different Microarray Platforms
    • Fan XH, Lobenhofer EK, Chen MJ, Shi WW, Huang JP, et al. (2010) Consistency of Predictive Signature Genes and Classifiers Generated Using Different Microarray Platforms. Pharmacogenomics J 10: 247-257.
    • (2010) Pharmacogenomics J , vol.10 , pp. 247-257
    • Fan, X.H.1    Lobenhofer, E.K.2    Chen, M.J.3    Shi, W.W.4    Huang, J.P.5
  • 21
    • 0035845511 scopus 로고    scopus 로고
    • Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications
    • Sorlie T, Perou CM, Tibshirani R, Aas T, Geisler S, et al. (2001) Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci U S A 98: 10869-10874.
    • (2001) Proc Natl Acad Sci U S A , vol.98 , pp. 10869-10874
    • Sorlie, T.1    Perou, C.M.2    Tibshirani, R.3    Aas, T.4    Geisler, S.5
  • 23
    • 47949114934 scopus 로고    scopus 로고
    • Genes related to apoptosis predict necrosis of the liver as a phenotype observed in rats exposed to a compendium of hepatotoxicants
    • Huang L, Heinloth AN, Zeng ZB, Paules RS, Bushel PR (2008) Genes related to apoptosis predict necrosis of the liver as a phenotype observed in rats exposed to a compendium of hepatotoxicants. BMC Genomics 9: 288-303.
    • (2008) BMC Genomics , vol.9 , pp. 288-303
    • Huang, L.1    Heinloth, A.N.2    Zeng, Z.B.3    Paules, R.S.4    Bushel, P.R.5
  • 25
    • 33748150984 scopus 로고    scopus 로고
    • Fuzzy KNN for predicting membrane protein types from pseudo-amino acid composition
    • Shen HB, Yang J, Chou KC (2006) Fuzzy KNN for predicting membrane protein types from pseudo-amino acid composition. J Theor Biol 240: 9-13.
    • (2006) J Theor Biol , vol.240 , pp. 9-13
    • Shen, H.B.1    Yang, J.2    Chou, K.C.3
  • 26
    • 0003922190 scopus 로고    scopus 로고
    • Pattern classification
    • NY, USA: John Wiley & Sons
    • Richard OD, Peter EH, David GS (2000) Pattern classification. NY, USA: John Wiley & Sons.
    • (2000)
    • Richard, O.D.1    Peter, E.H.2    David, G.S.3
  • 27
    • 0003710380 scopus 로고    scopus 로고
    • LIBSVM: A library for support vector machines
    • Software available at
    • Chang C-C, Lin C-J (2001) LIBSVM: a library for support vector machines. Software available at http://www.csie.ntu.edu.tw/,cjlin/libsvm.
    • (2001)
    • Chang, C.-C.1    Lin, C.-J.2
  • 28
    • 47249149840 scopus 로고    scopus 로고
    • Gene expression response in target organ and whole blood varies as a function of target organ injury phenotype
    • Lobenhofer EK, Auman JT, Blackshear PE, Boorman GA, Bushel PR, et al. (2008) Gene expression response in target organ and whole blood varies as a function of target organ injury phenotype. Genome Biol 9: R100.
    • (2008) Genome Biol , vol.9
    • Lobenhofer, E.K.1    Auman, J.T.2    Blackshear, P.E.3    Boorman, G.A.4    Bushel, P.R.5
  • 29
    • 33845781014 scopus 로고    scopus 로고
    • Application of visualization tools to the analysis of histopathological data enhances biological insight and interpretation
    • Lobenhofer EK, Boorman GA, Phillips KL, Heinloth AN, Malarkey DE, et al. (2006) Application of visualization tools to the analysis of histopathological data enhances biological insight and interpretation. Toxicol Pathol 34: 921-928.
    • (2006) Toxicol Pathol , vol.34 , pp. 921-928
    • Lobenhofer, E.K.1    Boorman, G.A.2    Phillips, K.L.3    Heinloth, A.N.4    Malarkey, D.E.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.