메뉴 건너뛰기




Volumn 12, Issue SUPPL. 10, 2011, Pages

Selecting a single model or combining multiple models for microarray-based classifier development? - A comparative analysis based on large and diverse datasets generated from the MAQC-II project

Author keywords

[No Author keywords available]

Indexed keywords

BETTER PERFORMANCE; CLINICAL APPLICATION; CLINICAL PRACTICES; COMPARATIVE ANALYSIS; ENSEMBLE MODELING; PREDICTIVE MODELS; PREDICTIVE PERFORMANCE; TOXICOLOGICAL RESEARCH;

EID: 80054120281     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-S10-S3     Document Type: Article
Times cited : (18)

References (36)
  • 1
    • 0035977845 scopus 로고    scopus 로고
    • Microarray analysis of hepatotoxins in vitro reveals a correlation between gene expression profiles and mechanisms of toxicity
    • 10.1016/S0378-4274(01)00267-3, 11323195
    • Waring JF, Ciurlionis R, Jolly RA, Heindel M, Ulrich RG. Microarray analysis of hepatotoxins in vitro reveals a correlation between gene expression profiles and mechanisms of toxicity. Toxicol Lett 2001, 120(1-3):359-368. 10.1016/S0378-4274(01)00267-3, 11323195.
    • (2001) Toxicol Lett , vol.120 , Issue.1-3 , pp. 359-368
    • Waring, J.F.1    Ciurlionis, R.2    Jolly, R.A.3    Heindel, M.4    Ulrich, R.G.5
  • 2
    • 0035092715 scopus 로고    scopus 로고
    • Challenges and limitations of gene expression profiling in mechanistic and predictive toxicology
    • 10.1093/toxsci/60.1.6, 11222867
    • Fielden MR, Zacharewski TR. Challenges and limitations of gene expression profiling in mechanistic and predictive toxicology. Toxicol Sci 2001, 60(1):6-10. 10.1093/toxsci/60.1.6, 11222867.
    • (2001) Toxicol Sci , vol.60 , Issue.1 , pp. 6-10
    • Fielden, M.R.1    Zacharewski, T.R.2
  • 3
    • 0033569406 scopus 로고    scopus 로고
    • Molecular classification of cancer: class discovery and class prediction by gene expression monitoring
    • 10.1126/science.286.5439.531, 10521349
    • Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 1999, 286(5439):531-537. 10.1126/science.286.5439.531, 10521349.
    • (1999) Science , vol.286 , Issue.5439 , pp. 531-537
    • Golub, T.R.1    Slonim, D.K.2    Tamayo, P.3    Huard, C.4    Gaasenbeek, M.5    Mesirov, J.P.6    Coller, H.7    Loh, M.L.8    Downing, J.R.9    Caligiuri, M.A.10
  • 4
    • 43249129586 scopus 로고    scopus 로고
    • Early diagnosis of pancreatic cancer: neutrophil gelatinase-associated lipocalin as a marker of pancreatic intraepithelial neoplasia
    • 10.1038/sj.bjc.6604329, 2391106, 18392050
    • Moniaux N, Chakraborty S, Yalniz M, Gonzalez J, Shostrom VK, Standop J, Lele SM, Ouellette M, Pour PM, Sasson AR, et al. Early diagnosis of pancreatic cancer: neutrophil gelatinase-associated lipocalin as a marker of pancreatic intraepithelial neoplasia. Br J Cancer 2008, 98(9):1540-1547. 10.1038/sj.bjc.6604329, 2391106, 18392050.
    • (2008) Br J Cancer , vol.98 , Issue.9 , pp. 1540-1547
    • Moniaux, N.1    Chakraborty, S.2    Yalniz, M.3    Gonzalez, J.4    Shostrom, V.K.5    Standop, J.6    Lele, S.M.7    Ouellette, M.8    Pour, P.M.9    Sasson, A.R.10
  • 5
    • 33947225176 scopus 로고    scopus 로고
    • Identification of candidate molecular markers predicting sensitivity in solid tumors to dasatinib: rationale for patient selection
    • 10.1158/0008-5472.CAN-06-3633, 17332353
    • Huang F, Reeves K, Han X, Fairchild C, Platero S, Wong TW, Lee F, Shaw P, Clark E. Identification of candidate molecular markers predicting sensitivity in solid tumors to dasatinib: rationale for patient selection. Cancer Res 2007, 67(5):2226-2238. 10.1158/0008-5472.CAN-06-3633, 17332353.
    • (2007) Cancer Res , vol.67 , Issue.5 , pp. 2226-2238
    • Huang, F.1    Reeves, K.2    Han, X.3    Fairchild, C.4    Platero, S.5    Wong, T.W.6    Lee, F.7    Shaw, P.8    Clark, E.9
  • 7
    • 20844444779 scopus 로고    scopus 로고
    • Idiosyncratic drug hepatotoxicity
    • 10.1038/nrd1750, 15931258
    • Kaplowitz N. Idiosyncratic drug hepatotoxicity. Nat Rev Drug Discov 2005, 4(6):489-499. 10.1038/nrd1750, 15931258.
    • (2005) Nat Rev Drug Discov , vol.4 , Issue.6 , pp. 489-499
    • Kaplowitz, N.1
  • 9
    • 33846978784 scopus 로고    scopus 로고
    • Critical review of published microarray studies for cancer outcome and guidelines on statistical analysis and reporting
    • 10.1093/jnci/djk018, 17227998
    • Dupuy A, Simon RM. Critical review of published microarray studies for cancer outcome and guidelines on statistical analysis and reporting. J Natl Cancer Inst 2007, 99(2):147-157. 10.1093/jnci/djk018, 17227998.
    • (2007) J Natl Cancer Inst , vol.99 , Issue.2 , pp. 147-157
    • Dupuy, A.1    Simon, R.M.2
  • 10
    • 13444249852 scopus 로고    scopus 로고
    • Prediction of cancer outcome with microarrays: a multiple random validation strategy
    • 10.1016/S0140-6736(05)17866-0, 15705458
    • Michiels S, Koscielny S, Hill C. Prediction of cancer outcome with microarrays: a multiple random validation strategy. Lancet 2005, 365(9458):488-492. 10.1016/S0140-6736(05)17866-0, 15705458.
    • (2005) Lancet , vol.365 , Issue.9458 , pp. 488-492
    • Michiels, S.1    Koscielny, S.2    Hill, C.3
  • 12
    • 0042822243 scopus 로고    scopus 로고
    • Using DNA microarrays for diagnostic and prognostic prediction
    • 10.1586/14737159.3.5.587, 14510179
    • Simon R. Using DNA microarrays for diagnostic and prognostic prediction. Expert Rev Mol Diagn 2003, 3(5):587-595. 10.1586/14737159.3.5.587, 14510179.
    • (2003) Expert Rev Mol Diagn , vol.3 , Issue.5 , pp. 587-595
    • Simon, R.1
  • 13
    • 0037245343 scopus 로고    scopus 로고
    • Pitfalls in the use of DNA microarray data for diagnostic and prognostic classification
    • 10.1093/jnci/95.1.14, 12509396
    • Simon R, Radmacher MD, Dobbin K, McShane LM. Pitfalls in the use of DNA microarray data for diagnostic and prognostic classification. J Natl Cancer Inst 2003, 95(1):14-18. 10.1093/jnci/95.1.14, 12509396.
    • (2003) J Natl Cancer Inst , vol.95 , Issue.1 , pp. 14-18
    • Simon, R.1    Radmacher, M.D.2    Dobbin, K.3    McShane, L.M.4
  • 14
    • 1342330535 scopus 로고    scopus 로고
    • Is cross-validation valid for small-sample microarray classification?
    • 10.1093/bioinformatics/btg419, 14960464
    • Braga-Neto UM, Dougherty ER. Is cross-validation valid for small-sample microarray classification?. Bioinformatics 2004, 20(3):374-380. 10.1093/bioinformatics/btg419, 14960464.
    • (2004) Bioinformatics , vol.20 , Issue.3 , pp. 374-380
    • Braga-Neto, U.M.1    Dougherty, E.R.2
  • 15
    • 33644860703 scopus 로고    scopus 로고
    • Bias in error estimation when using cross-validation for model selection
    • 10.1186/1471-2105-7-91, 1397873, 16504092
    • Varma S, Simon R. Bias in error estimation when using cross-validation for model selection. BMC Bioinformatics 2006, 7:91. 10.1186/1471-2105-7-91, 1397873, 16504092.
    • (2006) BMC Bioinformatics , vol.7 , pp. 91
    • Varma, S.1    Simon, R.2
  • 17
  • 19
    • 13444282534 scopus 로고    scopus 로고
    • Outcome signature genes in breast cancer: is there a unique set?
    • 10.1093/bioinformatics/bth469, 15308542
    • Ein-Dor L, Kela I, Getz G, Givol D, Domany E. Outcome signature genes in breast cancer: is there a unique set?. Bioinformatics 2005, 21(2):171-178. 10.1093/bioinformatics/bth469, 15308542.
    • (2005) Bioinformatics , vol.21 , Issue.2 , pp. 171-178
    • Ein-Dor, L.1    Kela, I.2    Getz, G.3    Givol, D.4    Domany, E.5
  • 20
    • 45249128876 scopus 로고
    • Combining forecasts: A review and annotated bibliography
    • Clemen R. Combining forecasts: A review and annotated bibliography. Journal of Forecasting 1989, 5:559-583.
    • (1989) Journal of Forecasting , vol.5 , pp. 559-583
    • Clemen, R.1
  • 21
    • 5444232094 scopus 로고    scopus 로고
    • Validated QSAR prediction of OH tropospheric degradation of VOCs: splitting into training-test sets and consensus modeling
    • Gramatica P, Pilutti P, Papa E. Validated QSAR prediction of OH tropospheric degradation of VOCs: splitting into training-test sets and consensus modeling. J Chem Inf Comput Sci 2004, 44(5):1794-1802.
    • (2004) J Chem Inf Comput Sci , vol.44 , Issue.5 , pp. 1794-1802
    • Gramatica, P.1    Pilutti, P.2    Papa, E.3
  • 22
    • 2942596534 scopus 로고    scopus 로고
    • Ensemble machine learning on gene expression data for cancer classification
    • Tan AC, Gilbert D. Ensemble machine learning on gene expression data for cancer classification. Appl Bioinformatics 2003, 2(3 Suppl):S75-83.
    • (2003) Appl Bioinformatics , vol.2 , Issue.3 SUPPL.
    • Tan, A.C.1    Gilbert, D.2
  • 23
    • 33846858448 scopus 로고    scopus 로고
    • Consensus analysis of multiple classifiers using non-repetitive variables: diagnostic application to microarray gene expression data
    • 10.1016/j.compbiolchem.2007.01.001, 17303535
    • Su Z, Hong H, Perkins R, Shao X, Cai W, Tong W. Consensus analysis of multiple classifiers using non-repetitive variables: diagnostic application to microarray gene expression data. Comput Biol Chem 2007, 31(1):48-56. 10.1016/j.compbiolchem.2007.01.001, 17303535.
    • (2007) Comput Biol Chem , vol.31 , Issue.1 , pp. 48-56
    • Su, Z.1    Hong, H.2    Perkins, R.3    Shao, X.4    Cai, W.5    Tong, W.6
  • 24
    • 78650735473 scopus 로고    scopus 로고
    • The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models
    • 10.1038/nbt.1665, 20676074
    • Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, et al. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol 2010, 28(8):827-838. 10.1038/nbt.1665, 20676074.
    • (2010) Nat Biotechnol , vol.28 , Issue.8 , pp. 827-838
    • Shi, L.1    Campbell, G.2    Jones, W.D.3    Campagne, F.4    Wen, Z.5    Walker, S.J.6    Su, Z.7    Chu, T.M.8    Goodsaid, F.M.9    Pusztai, L.10
  • 25
    • 34347250516 scopus 로고    scopus 로고
    • Application of genomic biomarkers to predict increased lung tumor incidence in 2-year rodent cancer bioassays
    • 10.1093/toxsci/kfm023, 17311802
    • Thomas RS, Pluta L, Yang L, Halsey TA. Application of genomic biomarkers to predict increased lung tumor incidence in 2-year rodent cancer bioassays. Toxicol Sci 2007, 97(1):55-64. 10.1093/toxsci/kfm023, 17311802.
    • (2007) Toxicol Sci , vol.97 , Issue.1 , pp. 55-64
    • Thomas, R.S.1    Pluta, L.2    Yang, L.3    Halsey, T.A.4
  • 26
    • 34547881497 scopus 로고    scopus 로고
    • A gene expression biomarker provides early prediction and mechanistic assessment of hepatic tumor induction by nongenotoxic chemicals
    • 10.1093/toxsci/kfm156, 17557906
    • Fielden MR, Brennan R, Gollub J. A gene expression biomarker provides early prediction and mechanistic assessment of hepatic tumor induction by nongenotoxic chemicals. Toxicol Sci 2007, 99(1):90-100. 10.1093/toxsci/kfm156, 17557906.
    • (2007) Toxicol Sci , vol.99 , Issue.1 , pp. 90-100
    • Fielden, M.R.1    Brennan, R.2    Gollub, J.3
  • 28
    • 33749030177 scopus 로고    scopus 로고
    • Pharmacogenomic predictor of sensitivity to preoperative chemotherapy with paclitaxel and fluorouracil, doxorubicin, and cyclophosphamide in breast cancer
    • 10.1200/JCO.2006.05.6861, 16896004
    • Hess KR, Anderson K, Symmans WF, Valero V, Ibrahim N, Mejia JA, Booser D, Theriault RL, Buzdar AU, Dempsey PJ, et al. Pharmacogenomic predictor of sensitivity to preoperative chemotherapy with paclitaxel and fluorouracil, doxorubicin, and cyclophosphamide in breast cancer. J Clin Oncol 2006, 24(26):4236-4244. 10.1200/JCO.2006.05.6861, 16896004.
    • (2006) J Clin Oncol , vol.24 , Issue.26 , pp. 4236-4244
    • Hess, K.R.1    Anderson, K.2    Symmans, W.F.3    Valero, V.4    Ibrahim, N.5    Mejia, J.A.6    Booser, D.7    Theriault, R.L.8    Buzdar, A.U.9    Dempsey, P.J.10
  • 30
    • 33947217497 scopus 로고    scopus 로고
    • A validated gene expression model of high-risk multiple myeloma is defined by deregulated expression of genes mapping to chromosome 1
    • 10.1182/blood-2006-07-038430, 17105813
    • Shaughnessy JD, Zhan F, Burington BE, Huang Y, Colla S, Hanamura I, Stewart JP, Kordsmeier B, Randolph C, Williams DR, et al. A validated gene expression model of high-risk multiple myeloma is defined by deregulated expression of genes mapping to chromosome 1. Blood 2007, 109(6):2276-2284. 10.1182/blood-2006-07-038430, 17105813.
    • (2007) Blood , vol.109 , Issue.6 , pp. 2276-2284
    • Shaughnessy, J.D.1    Zhan, F.2    Burington, B.E.3    Huang, Y.4    Colla, S.5    Hanamura, I.6    Stewart, J.P.7    Kordsmeier, B.8    Randolph, C.9    Williams, D.R.10
  • 31
    • 33750963337 scopus 로고    scopus 로고
    • Customized oligonucleotide microarray gene expression-based classification of neuroblastoma patients outperforms current clinical risk stratification
    • 10.1200/JCO.2006.06.1879, 17075126
    • Oberthuer A, Berthold F, Warnat P, Hero B, Kahlert Y, Spitz R, Ernestus K, Konig R, Haas S, Eils R, et al. Customized oligonucleotide microarray gene expression-based classification of neuroblastoma patients outperforms current clinical risk stratification. J Clin Oncol 2006, 24(31):5070-5078. 10.1200/JCO.2006.06.1879, 17075126.
    • (2006) J Clin Oncol , vol.24 , Issue.31 , pp. 5070-5078
    • Oberthuer, A.1    Berthold, F.2    Warnat, P.3    Hero, B.4    Kahlert, Y.5    Spitz, R.6    Ernestus, K.7    Konig, R.8    Haas, S.9    Eils, R.10
  • 32
    • 0035942271 scopus 로고    scopus 로고
    • Significance analysis of microarrays applied to the ionizing radiation response
    • 10.1073/pnas.091062498, 33173, 11309499
    • Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 2001, 98(9):5116-5121. 10.1073/pnas.091062498, 33173, 11309499.
    • (2001) Proc Natl Acad Sci U S A , vol.98 , Issue.9 , pp. 5116-5121
    • Tusher, V.G.1    Tibshirani, R.2    Chu, G.3
  • 33
    • 84855726604 scopus 로고    scopus 로고
    • R: A language and environment for statistical computing
    • Vienna, Austria ISBN 3-900051-07-0
    • Team RDC. R: A language and environment for statistical computing. R Foundation for Statistical computing 2010, Vienna, Austria ISBN 3-900051-07-0., http://www.R-project.org
    • (2010) R Foundation for Statistical computing
    • Team, R.D.C.1
  • 34
    • 33746454738 scopus 로고    scopus 로고
    • KlaR analyzing German business cycle
    • Springer-Verlag, Berlin, Baier, D, Decker, R and Schmitd-Thieme, L
    • Weihs C, Ligges U, Luebke K, Rabbe N. klaR analyzing German business cycle. Data Analysis and Decision Support 2005, 335-343. Springer-Verlag, Berlin, Baier, D, Decker, R and Schmitd-Thieme, L.
    • (2005) Data Analysis and Decision Support , pp. 335-343
    • Weihs, C.1    Ligges, U.2    Luebke, K.3    Rabbe, N.4
  • 36
    • 33846809281 scopus 로고    scopus 로고
    • Statistical external validation and consensus modeling: a QSPR case study for Koc prediction
    • 10.1016/j.jmgm.2006.06.005, 16890002
    • Gramatica P, Giani E, Papa E. Statistical external validation and consensus modeling: a QSPR case study for Koc prediction. J Mol Graph Model 2007, 25(6):755-766. 10.1016/j.jmgm.2006.06.005, 16890002.
    • (2007) J Mol Graph Model , vol.25 , Issue.6 , pp. 755-766
    • Gramatica, P.1    Giani, E.2    Papa, E.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.