메뉴 건너뛰기




Volumn 5, Issue 3, 2004, Pages 229-237

Expression profiling - Best practices for data generation and interpretation in clinical trials: The Tumor Analysis Best Practices Working Group

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; CELL HETEROGENEITY; CLINICAL RESEARCH; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; INFORMATION PROCESSING; PRIORITY JOURNAL; QUALITY CONTROL; REVIEW; RNA ISOLATION; SIGNAL NOISE RATIO; SIGNAL PROCESSING; STANDARD; STATISTICAL ANALYSIS;

EID: 1542290446     PISSN: 14710056     EISSN: None     Source Type: Journal    
DOI: 10.1038/nrg1297     Document Type: Review
Times cited : (206)

References (32)
  • 1
    • 18344396568 scopus 로고    scopus 로고
    • Minimum information about a microarray experiment (MIAME) - Toward standards for microarray data
    • Brazma, A. et al. Minimum information about a microarray experiment (MIAME) - toward standards for microarray data. Nature Genet. 29, 365-371 (2001).
    • (2001) Nature Genet. , vol.29 , pp. 365-371
    • Brazma, A.1
  • 2
    • 0037163144 scopus 로고    scopus 로고
    • Design and implementation of microarray gene expression markup language (MAGE-ML)
    • RESEARCH0046.1-0046.9
    • Spellman, P. T. et al. Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol. 3, RESEARCH0046.1-0046.9 (2002).
    • (2002) Genome Biol. , vol.3
    • Spellman, P.T.1
  • 3
    • 0037246058 scopus 로고    scopus 로고
    • ArrayExpress - A public repository for microarray gene expression data at the EBI
    • Brazma, A. et al. ArrayExpress - a public repository for microarray gene expression data at the EBI. Nucleic Acids Res, 31, 68-71 (2003).
    • (2003) Nucleic Acids Res. , vol.31 , pp. 68-71
    • Brazma, A.1
  • 4
    • 0038366147 scopus 로고    scopus 로고
    • Slug is downstream of myoD: Identification of novel pathway members via temporal expression profiling
    • Zhao, P., Iezzi, S., Sartorelli, V., Dressman, D. & Hoffman, E. P. Slug is downstream of myoD: identification of novel pathway members via temporal expression profiling. J. Biol. Chem. 277, 20091-20101 (2002).
    • (2002) J. Biol. Chem. , vol.277 , pp. 20091-20101
    • Zhao, P.1    Iezzi, S.2    Sartorelli, V.3    Dressman, D.4    Hoffman, E.P.5
  • 5
    • 0037379603 scopus 로고    scopus 로고
    • Gene profiling in spinal cord injury shows role of cell cycle in neuronal death
    • Di Giovanni, S. et al. Gene profiling in spinal cord injury shows role of cell cycle in neuronal death. Ann. Neurol. 53, 454-468 (2003).
    • (2003) Ann. Neurol. , vol.53 , pp. 454-468
    • Di Giovanni, S.1
  • 6
    • 0141742369 scopus 로고    scopus 로고
    • Modeling of corticosteroid pharmacogenomics in rat liver using gene microarrays
    • Jin, J. Y., Almon, R. R., DuBois, D. C. & Jusko, W. J. Modeling of corticosteroid pharmacogenomics in rat liver using gene microarrays. J. Pharmacol. Exp. Ther. 307, 93-109 (2003).
    • (2003) J. Pharmacol. Exp. Ther. , vol.307 , pp. 93-109
    • Jin, J.Y.1    Almon, R.R.2    DuBois, D.C.3    Jusko, W.J.4
  • 7
    • 2942576225 scopus 로고    scopus 로고
    • Sources of variability and effect of experimental approach on expression profiling data interpretation
    • Bakay, M. et al. Sources of variability and effect of experimental approach on expression profiling data interpretation. BMC Bioinformat. 3, 4-15 (2002).
    • (2002) BMC Bioinformat. , vol.3 , pp. 4-15
    • Bakay, M.1
  • 8
    • 0037423133 scopus 로고    scopus 로고
    • Expression profiling of blood samples from an SU5416 Phase III metastatic colorectal cancer clinical trial: A novel strategy for biomarker identification
    • DePrimo, S. E. et al. Expression profiling of blood samples from an SU5416 Phase III metastatic colorectal cancer clinical trial: a novel strategy for biomarker identification. BMC Cancer 3, 3 (2003).
    • (2003) BMC Cancer , vol.3 , pp. 3
    • DePrimo, S.E.1
  • 9
    • 0037324949 scopus 로고    scopus 로고
    • Gene expression profile of serial samples of transformed B-cell lymphomas
    • de Vos, S. et al. Gene expression profile of serial samples of transformed B-cell lymphomas. Lab. Invest. 83, 271-285 (2003).
    • (2003) Lab. Invest. , vol.83 , pp. 271-285
    • De Vos, S.1
  • 10
    • 0038069114 scopus 로고    scopus 로고
    • Skeletal muscle dictates the fibrinolytic state after exercise training in overweight men with characteristics of metabolic syndrome
    • Hittel, D. S., Kraus, W. E. & Hoffman, E. P. Skeletal muscle dictates the fibrinolytic state after exercise training in overweight men with characteristics of metabolic syndrome. J. Physiol 548, 401-410 (2003).
    • (2003) J. Physiol , vol.548 , pp. 401-410
    • Hittel, D.S.1    Kraus, W.E.2    Hoffman, E.P.3
  • 11
    • 1542332873 scopus 로고    scopus 로고
    • Time- and exercise-dependent gene regulation in human skeletal muscle
    • Zambon, A. C. et al. Time- and exercise-dependent gene regulation in human skeletal muscle. Genome Biol. 4, R61 (2003).
    • (2003) Genome Biol. , vol.4
    • Zambon, A.C.1
  • 12
    • 2942576225 scopus 로고    scopus 로고
    • Sources of variability, and effect of experimental approach on expression profiling data interpretation
    • Bakay, M. et al. Sources of variability, and effect of experimental approach on expression profiling data interpretation. BMC Bioinformat. 3, 4-15 (2002).
    • (2002) BMC Bioinformat. , vol.3 , pp. 4-15
    • Bakay, M.1
  • 13
    • 0242485317 scopus 로고    scopus 로고
    • Gene microarray study corroborates proteomic findings in rodent islet cells
    • Cardozo, A. K. et al. Gene microarray study corroborates proteomic findings in rodent islet cells. J. Proteome Res. 2, 553-555 (2003).
    • (2003) J. Proteome Res. , vol.2 , pp. 553-555
    • Cardozo, A.K.1
  • 14
    • 0037452711 scopus 로고    scopus 로고
    • Gene expression and viral prodution in latently infected, resting CD4*T cells in viremic versus aviremic HIV-infected individuals
    • Chun, T. W. et al. Gene expression and viral prodution in latently infected, resting CD4*T cells in viremic versus aviremic HIV-infected individuals. Proc. Natl Acad. Sci. USA 100, 1908-1913 (2003).
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 1908-1913
    • Chun, T.W.1
  • 15
    • 0037868952 scopus 로고    scopus 로고
    • Single-cell microarray analysis in hippocampus CA1: Demonstration and validation of cellular heterogeneity
    • Kamme, F. et al. Single-cell microarray analysis in hippocampus CA1: demonstration and validation of cellular heterogeneity. J. Neurosci. 23, 3607-3615 (2003).
    • (2003) J. Neurosci. , vol.23 , pp. 3607-3615
    • Kamme, F.1
  • 16
    • 0034895165 scopus 로고    scopus 로고
    • Effects of ischemia on gene expression
    • Huang, J. et al. Effects of ischemia on gene expression. J. Surg. Res, 99, 222-227 (2001).
    • (2001) J. Surg. Res. , vol.99 , pp. 222-227
    • Huang, J.1
  • 17
    • 0347428688 scopus 로고    scopus 로고
    • Interactive color mosaic and dendrogram displays for signal/noise optimization in microarray data analysis
    • Seo, J. et al. Interactive color mosaic and dendrogram displays for signal/noise optimization in microarray data analysis, IEEE ICME 3, 461-462 (2003).
    • (2003) IEEE ICME , vol.3 , pp. 461-462
    • Seo, J.1
  • 18
    • 0042923097 scopus 로고    scopus 로고
    • Class prediction and discovery using gene microarray and proteomics mass spectroscopy data: Curses, caveats, cautions
    • Somorjai, R. L., Dolenko, B. & Baumgartner, R. Class prediction and discovery using gene microarray and proteomics mass spectroscopy data: curses, caveats, cautions. Bioinformatics 19, 1484-1491 (2003).
    • (2003) Bioinformatics , vol.19 , pp. 1484-1491
    • Somorjai, R.L.1    Dolenko, B.2    Baumgartner, R.3
  • 19
    • 0141483023 scopus 로고    scopus 로고
    • Probe selection for high-density oligonucleotide arrays
    • Mei, R. et al. Probe selection for high-density oligonucleotide arrays, Proc. Natl Acad. Sci. USA 100, 11237-11242 (2003).
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 11237-11242
    • Mei, R.1
  • 20
    • 17744413236 scopus 로고    scopus 로고
    • Model-based analysis of oligonucleotide arrays: Model validation, design issues and standard error application
    • RESEARCH0032
    • Li, C. & Hung Wong, W. Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol. 2, RESEARCH0032 (2001).
    • (2001) Genome Biol. , vol.2
    • Li, C.1    Hung Wong, W.2
  • 21
    • 12344280017 scopus 로고    scopus 로고
    • Summaries of Affymetrix GeneChip probe level data
    • Irizarry, R. A. et al. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 31, e15 (2003).
    • (2003) Nucleic Acids Res. , vol.31
    • Irizarry, R.A.1
  • 22
    • 0037316303 scopus 로고    scopus 로고
    • A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    • Bolstad, B. M., Irizarry, R. A., Astrand, M. & Speed, T. P. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19, 185-193 (2003).
    • (2003) Bioinformatics , vol.19 , pp. 185-193
    • Bolstad, B.M.1    Irizarry, R.A.2    Astrand, M.3    Speed, T.P.4
  • 23
    • 0037076322 scopus 로고    scopus 로고
    • Selection bias in gene extraction on the basis of microarray gene-expression data
    • Ambroise, C. & McLachlan, G. J. Selection bias in gene extraction on the basis of microarray gene-expression data. Proc. Natl Acad. Sci. USA 99, 6562-6566 (2002).
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 6562-6566
    • Ambroise, C.1    McLachlan, G.J.2
  • 24
    • 0035949684 scopus 로고    scopus 로고
    • Predicting the clinical status of human breast cancer utilizing gene expression profiles
    • West, M. et al. Predicting the clinical status of human breast cancer utilizing gene expression profiles. Proc. Natl Acad. Sci. USA 98, 11462-11467 (2001).
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 11462-11467
    • West, M.1
  • 25
    • 0035942271 scopus 로고    scopus 로고
    • Significance analysis of microarrays applied to the ionizing radiation response
    • Tusher, V., Tibshirani, R. & Chu, G. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci. USA 98, 5116-5124 (2001).
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 5116-5124
    • Tusher, V.1    Tibshirani, R.2    Chu, G.3
  • 26
    • 0037076272 scopus 로고    scopus 로고
    • Diagnosis of multiple cancer types by shrunken centroids of gene expression
    • Tibshirani, R., Hastie, T. Narasimhan, B. & Chu, G. Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc. Natl Acad. Sci. USA 99, 6567-6572 (2002).
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 6567-6572
    • Tibshirani, R.1    Hastie, T.2    Narasimhan, B.3    Chu, G.4
  • 27
    • 0037941536 scopus 로고    scopus 로고
    • Gene expression phenotypic models that predict the activity of oncogenic pathways
    • Huang, E. et al. Gene expression phenotypic models that predict the activity of oncogenic pathways. Nature Genet. 34, 226-230 (2003).
    • (2003) Nature Genet. , vol.34 , pp. 226-230
    • Huang, E.1
  • 28
    • 0038756375 scopus 로고    scopus 로고
    • Distinct gene expression phenotypes of cells lacking Rb and Rb family members
    • Black, E. P. et al. Distinct gene expression phenotypes of cells lacking Rb and Rb family members. Cancer Res. 63, 3716-3723 (2003).
    • (2003) Cancer Res. , vol.63 , pp. 3716-3723
    • Black, E.P.1
  • 29
    • 0038244058 scopus 로고    scopus 로고
    • Gene expression predictors of breast cancer outcomes
    • Huang, E. et al. Gene expression predictors of breast cancer outcomes. Lancet 361, 1590-1596 (2003).
    • (2003) Lancet , vol.361 , pp. 1590-1596
    • Huang, E.1
  • 30
    • 0034730140 scopus 로고    scopus 로고
    • Singular value decomposition for genome-wide expression data processing and modeling
    • Alter, O., Brown, P. O. & Botstein, D. Singular value decomposition for genome-wide expression data processing and modeling. Proc. Natl Acad. Sci. USA 97, 10101-10106 (2000).
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 10101-10106
    • Alter, O.1    Brown, P.O.2    Botstein, D.3
  • 31
    • 0242442735 scopus 로고    scopus 로고
    • The PEPR GeneChip data warehouse and implementation of a dynamic time series query tool (SGQT) with graphical interface
    • Chen, J. et al. The PEPR GeneChip data warehouse and implementation of a dynamic time series query tool (SGQT) with graphical interface. Nucleic Acids Res. 32, D578-D581 (2004).
    • (2004) Nucleic Acids Res. , vol.32
    • Chen, J.1
  • 32
    • 0242391946 scopus 로고    scopus 로고
    • In vivo multitissue corticosteroid microarray time series available online at Public Expression Profile Resource (PEPR)
    • Almon et al. In vivo multitissue corticosteroid microarray time series available online at Public Expression Profile Resource (PEPR). Pharmacogenomics 4, 791-799 (2003).
    • (2003) Pharmacogenomics , vol.4 , pp. 791-799
    • Almon1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.