{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T19:52:01Z","timestamp":1771012321395,"version":"3.50.1"},"reference-count":32,"publisher":"Springer Science and Business Media LLC","issue":"3","license":[{"start":{"date-parts":[[2004,3,1]],"date-time":"2004-03-01T00:00:00Z","timestamp":1078099200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Nat Rev Genet"],"published-print":{"date-parts":[[2004,3]]},"DOI":"10.1038\/nrg1297","type":"journal-article","created":{"date-parts":[[2004,2,17]],"date-time":"2004-02-17T20:27:37Z","timestamp":1077049657000},"page":"229-237","source":"Crossref","is-referenced-by-count":182,"title":["Expression profiling \u2014 best practices for data generation and interpretation in clinical trials"],"prefix":"10.1038","volume":"5","author":[{"name":"The Tumor Analysis Best Practices Working Group","sequence":"first","affiliation":[]}],"member":"297","reference":[{"key":"BFnrg1297_CR1","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1038\/ng1201-365","volume":"29","author":"A Brazma","year":"2001","unstructured":"Brazma, A. et al. Minimum information about a microarray experiment (MIAME) \u2014 toward standards for microarray data. Nature Genet. 29, 365\u2013371 (2001).","journal-title":"Nature Genet."},{"key":"BFnrg1297_CR2","doi-asserted-by":"publisher","first-page":"RESEARCH0046.1-","DOI":"10.1186\/gb-2002-3-9-research0046","volume":"3","author":"PT Spellman","year":"2002","unstructured":"Spellman, P. T. et al. Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol. 3, RESEARCH0046.1-0046.9 (2002).","journal-title":"Genome Biol."},{"key":"BFnrg1297_CR3","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1093\/nar\/gkg091","volume":"31","author":"A Brazma","year":"2003","unstructured":"Brazma, A. et al. ArrayExpress \u2014 a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 31, 68\u201371 (2003).","journal-title":"Nucleic Acids Res."},{"key":"BFnrg1297_CR4","first-page":"20091","volume":"277","author":"P Zhao","year":"2002","unstructured":"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\u201320101 (2002).","journal-title":"J. Biol. Chem."},{"key":"BFnrg1297_CR5","doi-asserted-by":"publisher","first-page":"454","DOI":"10.1002\/ana.10472","volume":"53","author":"S Di Giovanni","year":"2003","unstructured":"Di Giovanni, S. et al. Gene profiling in spinal cord injury shows role of cell cycle in neuronal death. Ann. Neurol. 53, 454\u2013468 (2003).","journal-title":"Ann. Neurol."},{"key":"BFnrg1297_CR6","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1124\/jpet.103.053256","volume":"307","author":"JY Jin","year":"2003","unstructured":"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\u2013109 (2003).","journal-title":"J. Pharmacol. Exp. Ther."},{"key":"BFnrg1297_CR7","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1186\/1471-2105-3-4","volume":"3","author":"M Bakay","year":"2002","unstructured":"Bakay, M. et al. Sources of variability and effect of experimental approach on expression profiling data interpretation. BMC Bioinformat. 3, 4\u201315 (2002).","journal-title":"BMC Bioinformat."},{"key":"BFnrg1297_CR8","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1186\/1471-2407-3-3","volume":"3","author":"SE DePrimo","year":"2003","unstructured":"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).","journal-title":"BMC Cancer"},{"key":"BFnrg1297_CR9","doi-asserted-by":"publisher","first-page":"271","DOI":"10.1097\/01.LAB.0000053913.85892.E9","volume":"83","author":"S de Vos","year":"2003","unstructured":"de Vos, S. et al. Gene expression profile of serial samples of transformed B-cell lymphomas. Lab. Invest. 83, 271\u2013285 (2003).","journal-title":"Lab. Invest."},{"key":"BFnrg1297_CR10","doi-asserted-by":"publisher","first-page":"401","DOI":"10.1113\/jphysiol.2002.036616","volume":"548","author":"DS Hittel","year":"2003","unstructured":"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\u2013410 (2003).","journal-title":"J. Physiol."},{"key":"BFnrg1297_CR11","doi-asserted-by":"publisher","first-page":"R61","DOI":"10.1186\/gb-2003-4-10-r61","volume":"4","author":"AC Zambon","year":"2003","unstructured":"Zambon, A. C. et al. Time- and exercise-dependent gene regulation in human skeletal muscle. Genome Biol. 4, R61 (2003).","journal-title":"Genome Biol."},{"key":"BFnrg1297_CR12","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1186\/1471-2105-3-4","volume":"3","author":"M Bakay","year":"2002","unstructured":"Bakay, M. et al. Sources of variability and effect of experimental approach on expression profiling data interpretation. BMC Bioinformat. 3, 4\u201315 (2002).","journal-title":"BMC Bioinformat."},{"key":"BFnrg1297_CR13","doi-asserted-by":"publisher","first-page":"553","DOI":"10.1021\/pr034029o","volume":"2","author":"AK Cardozo","year":"2003","unstructured":"Cardozo, A. K. et al. Gene microarray study corroborates proteomic findings in rodent islet cells. J. Proteome Res. 2, 553\u2013555 (2003).","journal-title":"J. Proteome Res."},{"key":"BFnrg1297_CR14","doi-asserted-by":"publisher","first-page":"1908","DOI":"10.1073\/pnas.0437640100","volume":"100","author":"TW Chun","year":"2003","unstructured":"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\u20131913 (2003).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFnrg1297_CR15","doi-asserted-by":"publisher","first-page":"3607","DOI":"10.1523\/JNEUROSCI.23-09-03607.2003","volume":"23","author":"F Kamme","year":"2003","unstructured":"Kamme, F. et al. Single-cell microarray analysis in hippocampus CA1: demonstration and validation of cellular heterogeneity. J. Neurosci. 23, 3607\u20133615 (2003).","journal-title":"J. Neurosci."},{"key":"BFnrg1297_CR16","doi-asserted-by":"publisher","first-page":"222","DOI":"10.1006\/jsre.2001.6195","volume":"99","author":"J Huang","year":"2001","unstructured":"Huang, J. et al. Effects of ischemia on gene expression. J. Surg. Res. 99, 222\u2013227 (2001).","journal-title":"J. Surg. Res."},{"key":"BFnrg1297_CR17","first-page":"461","volume":"3","author":"J Seo","year":"2003","unstructured":"Seo, J. et al. Interactive color mosaic and dendrogram displays for signal\/noise optimization in microarray data analysis. IEEE ICME 3, 461\u2013462 (2003).","journal-title":"IEEE ICME"},{"key":"BFnrg1297_CR18","doi-asserted-by":"publisher","first-page":"1484","DOI":"10.1093\/bioinformatics\/btg182","volume":"19","author":"RL Somorjai","year":"2003","unstructured":"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\u20131491 (2003).","journal-title":"Bioinformatics"},{"key":"BFnrg1297_CR19","doi-asserted-by":"publisher","first-page":"11237","DOI":"10.1073\/pnas.1534744100","volume":"100","author":"R Mei","year":"2003","unstructured":"Mei, R. et al. Probe selection for high-density oligonucleotide arrays. Proc. Natl Acad. Sci. USA 100, 11237\u201311242 (2003).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFnrg1297_CR20","doi-asserted-by":"crossref","first-page":"RESEARCH0032","DOI":"10.1186\/gb-2001-2-10-reports0032","volume":"2","author":"C Li","year":"2001","unstructured":"Li, C. & Hung Wong, W. Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol. 2, RESEARCH0032 (2001).","journal-title":"Genome Biol."},{"key":"BFnrg1297_CR21","doi-asserted-by":"publisher","first-page":"e15","DOI":"10.1093\/nar\/gng015","volume":"31","author":"RA Irizarry","year":"2003","unstructured":"Irizarry, R. A. et al. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 31, e15 (2003).","journal-title":"Nucleic Acids Res."},{"key":"BFnrg1297_CR22","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1093\/bioinformatics\/19.2.185","volume":"19","author":"BM Bolstad","year":"2003","unstructured":"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\u2013193 (2003).","journal-title":"Bioinformatics"},{"key":"BFnrg1297_CR23","doi-asserted-by":"publisher","first-page":"6562","DOI":"10.1073\/pnas.102102699","volume":"99","author":"C Ambroise","year":"2002","unstructured":"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\u20136566 (2002).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFnrg1297_CR24","doi-asserted-by":"publisher","first-page":"11462","DOI":"10.1073\/pnas.201162998","volume":"98","author":"M West","year":"2001","unstructured":"West, M. et al. Predicting the clinical status of human breast cancer utilizing gene expression profiles. Proc. Natl Acad. Sci. USA 98, 11462\u201311467 (2001).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFnrg1297_CR25","doi-asserted-by":"publisher","first-page":"5116","DOI":"10.1073\/pnas.091062498","volume":"98","author":"V Tusher","year":"2001","unstructured":"Tusher, V., Tibshirani, R. & Chu, G. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci. USA 98, 5116\u20135124 (2001).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFnrg1297_CR26","doi-asserted-by":"publisher","first-page":"6567","DOI":"10.1073\/pnas.082099299","volume":"99","author":"R Tibshirani","year":"2002","unstructured":"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\u20136572 (2002).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFnrg1297_CR27","doi-asserted-by":"publisher","first-page":"226","DOI":"10.1038\/ng1167","volume":"34","author":"E Huang","year":"2003","unstructured":"Huang, E. et al. Gene expression phenotypic models that predict the activity of oncogenic pathways. Nature Genet. 34, 226\u2013230 (2003).","journal-title":"Nature Genet."},{"key":"BFnrg1297_CR28","first-page":"3716","volume":"63","author":"EP Black","year":"2003","unstructured":"Black, E. P. et al. Distinct gene expression phenotypes of cells lacking Rb and Rb family members. Cancer Res. 63, 3716\u20133723 (2003).","journal-title":"Cancer Res."},{"key":"BFnrg1297_CR29","doi-asserted-by":"publisher","first-page":"1590","DOI":"10.1016\/S0140-6736(03)13308-9","volume":"361","author":"E Huang","year":"2003","unstructured":"Huang, E. et al. Gene expression predictors of breast cancer outcomes. Lancet 361, 1590\u20131596 (2003).","journal-title":"Lancet"},{"key":"BFnrg1297_CR30","doi-asserted-by":"publisher","first-page":"10101","DOI":"10.1073\/pnas.97.18.10101","volume":"97","author":"O Alter","year":"2000","unstructured":"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\u201310106 (2000).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"BFnrg1297_CR31","doi-asserted-by":"publisher","first-page":"D578","DOI":"10.1093\/nar\/gkh003","volume":"32","author":"J Chen","year":"2004","unstructured":"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\u2013D581 (2004).","journal-title":"Nucleic Acids Res."},{"key":"BFnrg1297_CR32","doi-asserted-by":"publisher","first-page":"791","DOI":"10.1517\/phgs.4.6.791.22816","volume":"4","author":"Almon","year":"2003","unstructured":"Almon et al. In vivo multitissue corticosteroid microarray time series available online at Public Expression Profile Resource (PEPR). Pharmacogenomics 4, 791\u2013799 (2003).","journal-title":"Pharmacogenomics"}],"container-title":["Nature Reviews Genetics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/www.nature.com\/articles\/nrg1297.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/nrg1297","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/nrg1297.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,19]],"date-time":"2023-05-19T03:57:27Z","timestamp":1684468647000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/nrg1297"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2004,3]]},"references-count":32,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2004,3]]}},"alternative-id":["BFnrg1297"],"URL":"https:\/\/doi.org\/10.1038\/nrg1297","relation":{},"ISSN":["1471-0056","1471-0064"],"issn-type":[{"value":"1471-0056","type":"print"},{"value":"1471-0064","type":"electronic"}],"subject":[],"published":{"date-parts":[[2004,3]]}}}